
PFRMAT FRV1
AUTHOR 6776-3217-5205 M J E Sternberg
AUTHOR 6776-3217-5205 Imperial Cancer Research Fund
AUTHOR 6776-3217-5205 m.sternberg@icrf.icnet.uk
AUTHOR 6776-3217-5205 Details of all workers see below
REMARK ======================================================================
REMARK Threading results from FOLDFIT:
REMARK 
REMARK Work by Michael J E Sternberg (1), Paul A Bates (1), Andrew Lyall (2)
REMARK Robert B Russell (1), Mansoor A S Saqi (2) and Roger Sayle (2)
REMARK (1) Biomolecular Modelling Laboratory
REMARK Imperial Cancer Research Fund
REMARK Lincoln Inn Fields, London, WC2A 3PX, UK
REMARK Tel +44 - 171 - 269- 3565
REMARK Fax +44 - 171 - 269 - 3479
REMARK URL http://bonsai.lif.icnet.uk
REMARK E-mail m.sternberg@icrf.icnet.uk
REMARK E-mail p.bates@icrf.icnet.uk 
REMARK E-mail r.russell@icrf.icnet.uk
REMARK (2) Bioinformatics Group
REMARK Glaxo Medicines Research Centre
REMARK Gunnels Wood Road
REMARK Stevenage, Herts, SG1 2NY, UK
REMARK Tel +44 -1438 - 745745
REMARK Tel +44 -1438 - 763082
REMARK E-mail al28044@ggr.co.uk
REMARK E-mail mass15599@ggr.co.uk
REMARK E-mail ras32425@ggr.co.uk
REMARK ======================================================================
REMARK                       FOLDFIT
REMARK                       =======
REMARK The program was jointly and equally developed by the above two groups .
REMARK The program matches the (1) sequence, (2) predicted secondary structure
REMARK and (3) predicted burial of the unknown sequence
REMARK against a database of known structures detailing
REMARK (1) sequence, (2) actual and predicted secondary structure
REMARK and (3) actual and predicted burial.
REMARK The matches are scored by matrices empirically derived
REMARK from comparison of analogous and distantly homologous protein folds.
REMARK Searching is by a type I dynamic programming algorithm
REMARK with afine secondary-structure dependant gap penalties.
REMARK ======================================================================
REMARK ======================================================================
REMARK T0004 study
REMARK ======================================================================
REMARK
REMARK (1) An initial Smith-Waterman search with the sequence of T0004 
REMARK through sequences from the Brookhaven Protein Databank suggested 
REMARK a possible remote homology with a domain from HIV-1 reverse 
REMARK transcriptase (PDB code 1RTH chain A residues 435-516), which was 
REMARK subsequently found to be a member of the Ribonuclease H-like 
REMARK superfamily (as identified within SCOP).  FOLDFIT was used then 
REMARK to validate this functionally compelling similarity (both T0004 and 
REMARK this family of proteins are nucleotidyl transferases).
REMARK
REMARK (2) A consensus secondary structure assignment from multiply
REMARK aligned homologous sequences was made using results of DSC (King
REMARK & Sternberg, T0004 CASP Submission) PHD (Rost & Sander), SOMP 
REMARK (Geourjon & Deleage), NNPREDICT (Kneller, Harris & Cohen)
REMARK together with visual inspection.  A consensus prediction of 
REMARK secondary structure, together with accessibilities from PHD was 
REMARK used as input to FOLDFIT.
REMARK 
REMARK (3) FOLDFIT at present is unable to detect similarities of a 
REMARK small domain within a longer sequence.  In our template library, 
REMARK there was no representative of the core ribonuclease-H like fold.  
REMARK Accordingly, our template library was augmented to include two 
REMARK domain representatives of this fold superfamily (1ITG residues 55-150;
REMARK 2RN2 residues 2-71,99-155)
REMARK
REMARK (4) T0004 was scanned by FOLDFIT and the rank order of the PDB codes 
REMARK matched by FOLDFIT are listed below in decreasing order of probability.
REMARK One representative from the ribonuclase H like motif (1ITG) came top 
REMARK in the list of results from FOLDFIT, and was accordingly selected 
REMARK with 100 % confidence.
REMARK 
REMARK (5) For the matched fold, two alignments were submitted, the 
REMARK optimal and the first sub-optimal using the algorithm of Saqi &
REMARK Sternberg (J.Mol.Biol. 219, 727-732, 1991).  The probabilities   
REMARK for the alignments were chosen subjectively.  
REMARK
REMARK (6) Intriguingly, the location of two aspatate residues often
REMARK found within T0004 homologues were roughly aligned with two aspartates
REMARK generally conserved within the ribonuclease H like superfamily.
REMARK 
REMARK ======================================================================
REMARK
REMARK Sequence considered one domain
REMARK ========================================================
SEQRES T0004 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYL
SEQRES T0004 QMGQEVPVKVLEVDRQGRIRLSIKEATEQSQPAA                
REMARK ========================================================
REMARK
REMARK 
REMARK =============================================================
REMARK 
STRSUB 1ITG - 1  55   140
STRSUB 1ITG - 2 154   209
STRSUB 2RN2 - 1   2    71
STRSUB 2RN2 - 1  99   155
STRSUB 2RN2 - 2  72    98
REMARK
TSCORE T0004 0 1.00   1ITG - 1 
TSCORE T0004 0 0.00   1TNM - 0 
TSCORE T0004 0 0.00   1TEN - 0 
TSCORE T0004 0 0.00   1ZAA C 0 
TSCORE T0004 0 0.00   1FNA - 0 
TSCORE T0004 0 0.00   1PAZ - 0 
TSCORE T0004 0 0.00   1FKB - 0 
TSCORE T0004 0 0.00   1ABA - 0 
TSCORE T0004 0 0.00   1PND - 0 
TSCORE T0004 0 0.00   1MSA A 0 
TSCORE T0004 0 0.00   1HIV A 0 
TSCORE T0004 0 0.00   3TRX - 0 
TSCORE T0004 0 0.00   1DIF A 0 
TSCORE T0004 0 0.00   1HSB B 0 
TSCORE T0004 0 0.00   2KAU B 0 
TSCORE T0004 0 0.00   1KJC - 0 
TSCORE T0004 0 0.00   1SNC - 0 
TSCORE T0004 0 0.00   1CD8 - 0 
TSCORE T0004 0 0.00   2TRX A 0 
TSCORE T0004 0 0.00   1TPG - 0 
TSCORE T0004 0 0.00   1POH - 0 
TSCORE T0004 0 0.00   3CHY - 0 
TSCORE T0004 0 0.00   2FXB - 0 
TSCORE T0004 0 0.00   2AZA A 0 
TSCORE T0004 0 0.00   1YCC - 0 
TSCORE T0004 0 0.00   3SIC I 0 
TSCORE T0004 0 0.00   1PDG A 0 
TSCORE T0004 0 0.00   1EXG - 0 
TSCORE T0004 0 0.00   1TLK - 0 
TSCORE T0004 0 0.00   4FXN - 0 
TSCORE T0004 0 0.00   1MJC - 0 
TSCORE T0004 0 0.00   1FRD - 0 
TSCORE T0004 0 0.00   3RUB S 0 
TSCORE T0004 0 0.00   1LKK A 0 
TSCORE T0004 0 0.00   1PK4 - 0 
TSCORE T0004 0 0.00   2RN2 - 1 
TSCORE T0004 0 0.00   1AYA A 0 
TSCORE T0004 0 0.00   1FBR - 0 
TSCORE T0004 0 0.00   1LTS D 0 
TSCORE T0004 0 0.00   1PYI A 0 
TSCORE T0004 0 0.00   1HCN B 0 
TSCORE T0004 0 0.00   1FIA B 0 
TSCORE T0004 0 0.00   1BFG - 0 
TSCORE T0004 0 0.00   1WAP A 0 
TSCORE T0004 0 0.00   2MSB A 0 
TSCORE T0004 0 0.00   451C - 0 
TSCORE T0004 0 0.00   2PNA - 0 
TSCORE T0004 0 0.00   2DRP A 0 
TSCORE T0004 0 0.00   1TTB A 0 
TSCORE T0004 0 0.00   1VIL - 0 
TSCORE T0004 0 0.00   1HUM A 0 
TSCORE T0004 0 0.00   1XXB A 0 
TSCORE T0004 0 0.00   2RSP A 0 
TSCORE T0004 0 0.00   1CHC - 0 
TSCORE T0004 0 0.00   2SN3 - 0 
TSCORE T0004 0 0.00   1CYX - 0 
TSCORE T0004 0 0.00   4FX2 - 0 
TSCORE T0004 0 0.00   1NCG - 0 
TSCORE T0004 0 0.00   5P21 - 0 
TSCORE T0004 0 0.00   1KPT A 0 
TSCORE T0004 0 0.00   2PLD A 0 
TSCORE T0004 0 0.00   1FIV A 0 
TSCORE T0004 0 0.00   1RSY - 0 
TSCORE T0004 0 0.00   3EBX - 0 
TSCORE T0004 0 0.00   1ICE B 0 
TSCORE T0004 0 0.00   1ACF - 0 
TSCORE T0004 0 0.00   1TIG - 0 
TSCORE T0004 0 0.00   1TIF - 0 
TSCORE T0004 0 0.00   1LAB - 0 
TSCORE T0004 0 0.00   1GPR - 0 
TSCORE T0004 0 0.00   1SLT B 0 
TSCORE T0004 0 0.00   5PAL - 0 
TSCORE T0004 0 0.00   1COB A 0 
TSCORE T0004 0 0.00   1PNE - 0 
TSCORE T0004 0 0.00   1FDD - 0 
TSCORE T0004 0 0.00   1UBI - 0 
TSCORE T0004 0 0.00   1BTN - 0 
TSCORE T0004 0 0.00   1CMB A 0 
TSCORE T0004 0 0.00   1UDI I 0 
TSCORE T0004 0 0.00   2MCM - 0 
TSCORE T0004 0 0.00   1MDY A 0 
TSCORE T0004 0 0.00   1PHT - 0 
TSCORE T0004 0 0.00   1VCC - 0 
TSCORE T0004 0 0.00   1STF I 0 
TSCORE T0004 0 0.00   3B5C - 0 
TSCORE T0004 0 0.00   1AAK - 0 
TSCORE T0004 0 0.00   1DCH A 0 
TSCORE T0004 0 0.00   1PBA - 0 
TSCORE T0004 0 0.00   4CPV - 0 
TSCORE T0004 0 0.00   1DYN A 0 
TSCORE T0004 0 0.00   1PSP A 0 
TSCORE T0004 0 0.00   1BPK - 0 
TSCORE T0004 0 0.00   1GMF A 0 
TSCORE T0004 0 0.00   1LEA - 0 
TSCORE T0004 0 0.00   1PTX - 0 
TSCORE T0004 0 0.00   1CYI - 0 
TSCORE T0004 0 0.00   1PKP - 0 
TSCORE T0004 0 0.00   1HST A 0 
TSCORE T0004 0 0.00   1PIL - 0 
TSCORE T0004 0 0.00   1GTQ A 0 
TSCORE T0004 0 0.00   1I1B - 0 
TSCORE T0004 0 0.00   1HRE - 0 
TSCORE T0004 0 0.00   1ILR 1 0 
TSCORE T0004 0 0.00   1DIS - 0 
TSCORE T0004 0 0.00   1SAP - 0 
TSCORE T0004 0 0.00   1BOV A 0 
TSCORE T0004 0 0.00   2BOP A 0 
TSCORE T0004 0 0.00   2CDV - 0 
TSCORE T0004 0 0.00   1ONC - 0 
TSCORE T0004 0 0.00   1TGX A 0 
TSCORE T0004 0 0.00   1HSQ - 0 
TSCORE T0004 0 0.00   1LLI A 0 
TSCORE T0004 0 0.00   9RNT - 0 
TSCORE T0004 0 0.00   1PRT F 0 
TSCORE T0004 0 0.00   1OFV - 0 
TSCORE T0004 0 0.00   1FXR A 0 
TSCORE T0004 0 0.00   1PRT D 0 
TSCORE T0004 0 0.00   1ATA - 0 
TSCORE T0004 0 0.00   1LBA - 0 
TSCORE T0004 0 0.00   3IL8 - 0 
TSCORE T0004 0 0.00   1SMP I 0 
TSCORE T0004 0 0.00   1RND - 0 
TSCORE T0004 0 0.00   1ICE A 0 
TSCORE T0004 0 0.00   1BSR A 0 
TSCORE T0004 0 0.00   1RIS - 0 
TSCORE T0004 0 0.00   1HOE - 0 
TSCORE T0004 0 0.00   1NCF A 0 
TSCORE T0004 0 0.00   2CPL - 0 
TSCORE T0004 0 0.00   1FLX - 0 
TSCORE T0004 0 0.00   1ERG - 0 
TSCORE T0004 0 0.00   1AAL A 0 
TSCORE T0004 0 0.00   2CHS A 0 
TSCORE T0004 0 0.00   1BET - 0 
TSCORE T0004 0 0.00   1POA - 0 
TSCORE T0004 0 0.00   1HRY A 0 
TSCORE T0004 0 0.00   1AGI - 0 
TSCORE T0004 0 0.00   1ENH - 0 
TSCORE T0004 0 0.00   1GMP A 0 
TSCORE T0004 0 0.00   3AAH B 0 
TSCORE T0004 0 0.00   1CTF - 0 
TSCORE T0004 0 0.00   1CXC - 0 
TSCORE T0004 0 0.00   1HUR A 0 
TSCORE T0004 0 0.00   2SNV - 0 
TSCORE T0004 0 0.00   1PUC - 0 
TSCORE T0004 0 0.00   1HIP - 0 
TSCORE T0004 0 0.00   1ECM A 0 
TSCORE T0004 0 0.00   2IHL - 0 
TSCORE T0004 0 0.00   1APK - 0 
TSCORE T0004 0 0.00   1R69 - 0 
TSCORE T0004 0 0.00   1UTG - 0 
TSCORE T0004 0 0.00   1CC5 - 0 
TSCORE T0004 0 0.00   1HUL A 0 
TSCORE T0004 0 0.00   1MSC - 0 
TSCORE T0004 0 0.00   1SSR - 0 
TSCORE T0004 0 0.00   1PVC 4 0 
TSCORE T0004 0 0.00   1TNS - 0 
TSCORE T0004 0 0.00   1REG X 0 
TSCORE T0004 0 0.00   1MCA A 0 
TSCORE T0004 0 0.00   1HPI - 0 
TSCORE T0004 0 0.00   1OTG A 0 
TSCORE T0004 0 0.00   1TIE - 0 
TSCORE T0004 0 0.00   1DUP A 0 
TSCORE T0004 0 0.00   1NEQ - 0 
TSCORE T0004 0 0.00   1BRN L 0 
TSCORE T0004 0 0.00   1APL C 0 
TSCORE T0004 0 0.00   4GCR - 0 
TSCORE T0004 0 0.00   1LFA A 0 
TSCORE T0004 0 0.00   1CID - 0 
TSCORE T0004 0 0.00   1ABO A 0 
TSCORE T0004 0 0.00   1RFB A 0 
TSCORE T0004 0 0.00   1CSE I 0 
TSCORE T0004 0 0.00   1TNF A 0 
TSCORE T0004 0 0.00   1CDC B 0 
TSCORE T0004 0 0.00   1PTS A 0 
TSCORE T0004 0 0.00   1SHG - 0 
TSCORE T0004 0 0.00   1YPC I 0 
TSCORE T0004 0 0.00   1HCN A 0 
TSCORE T0004 0 0.00   1BGH - 0 
TSCORE T0004 0 0.00   1AAP A 0 
TSCORE T0004 0 0.00   1HCC - 0 
TSCORE T0004 0 0.00   1CAU B 0 
TSCORE T0004 0 0.00   3ITR - 0 
TSCORE T0004 0 0.00   1CDA A 0 
TSCORE T0004 0 0.00   1MHL A 0 
TSCORE T0004 0 0.00   1HYM A 0 
TSCORE T0004 0 0.00   1ESL - 0 
TSCORE T0004 0 0.00   2WRP R 0 
TSCORE T0004 0 0.00   1PDN C 0 
TSCORE T0004 0 0.00   2MHR - 0 
TSCORE T0004 0 0.00   1SCM A 0 
TSCORE T0004 0 0.00   1POC - 0 
TSCORE T0004 0 0.00   1HNR - 0 
TSCORE T0004 0 0.00   1CYN A 0 
TSCORE T0004 0 0.00   1VHH - 0 
TSCORE T0004 0 0.00   8DFR - 0 
TSCORE T0004 0 0.00   1LFB - 0 
TSCORE T0004 0 0.00   1ASU - 0 
TSCORE T0004 0 0.00   1CEW I 0 
TSCORE T0004 0 0.00   1GP1 A 0 
TSCORE T0004 0 0.00   1TFG - 0 
TSCORE T0004 0 0.00   1HYP - 0 
TSCORE T0004 0 0.00   1SPB P 0 
TSCORE T0004 0 0.00   1FXD - 0 
TSCORE T0004 0 0.00   1HLH A 0 
TSCORE T0004 0 0.00   1HCD - 0 
TSCORE T0004 0 0.00   1OTF A 0 
TSCORE T0004 0 0.00   2PF2 - 0 
TSCORE T0004 0 0.00   1TFI - 0 
TSCORE T0004 0 0.00   2HIP A 0 
TSCORE T0004 0 0.00   1PRR - 0 
TSCORE T0004 0 0.00   1EGF - 0 
TSCORE T0004 0 0.00   2KAU A 0 
TSCORE T0004 0 0.00   1TBP A 0 
TSCORE T0004 0 0.00   2PRD - 0 
TSCORE T0004 0 0.00   1PHR - 0 
TSCORE T0004 0 0.00   1COO - 0 
TSCORE T0004 0 0.00   4SGB I 0 
TSCORE T0004 0 0.00   1RBP - 0 
TSCORE T0004 0 0.00   8ATC B 0 
TSCORE T0004 0 0.00   1MUP - 0 
TSCORE T0004 0 0.00   2BBK L 0 
TSCORE T0004 0 0.00   1BBP A 0 
TSCORE T0004 0 0.00   1VMO A 0 
TSCORE T0004 0 0.00   1HJR A 0 
TSCORE T0004 0 0.00   1LCC A 0 
TSCORE T0004 0 0.00   2GF1 - 0 
TSCORE T0004 0 0.00   2PHY - 0 
TSCORE T0004 0 0.00   1L92 - 0 
TSCORE T0004 0 0.00   1WHT B 0 
TSCORE T0004 0 0.00   2APD - 0 
TSCORE T0004 0 0.00   1HPT - 0 
TSCORE T0004 0 0.00   1GAT A 0 
TSCORE T0004 0 0.00   1DSB A 0 
TSCORE T0004 0 0.00   1FOS E 0 
TSCORE T0004 0 0.00   1HCG B 0 
TSCORE T0004 0 0.00   1HTM D 0 
TSCORE T0004 0 0.00   1FOS F 0 
TSCORE T0004 0 0.00   1MOL A 0 
TSCORE T0004 0 0.00   3CD4 - 0 
TSCORE T0004 0 0.00   1AFA 1 0 
TSCORE T0004 0 0.00   1ITG - 2
TSCORE T0004 0 0.00   1LPB A 0 
TSCORE T0004 0 0.00   1GRJ - 0 
TSCORE T0004 0 0.00   1MLP A 0 
TSCORE T0004 0 0.00   2END - 0 
TSCORE T0004 0 0.00   1ALS - 0 
TSCORE T0004 0 0.00   8RXN A 0 
TSCORE T0004 0 0.00   2CCY A 0 
TSCORE T0004 0 0.00   1CGJ I 0 
TSCORE T0004 0 0.00   1BCX - 0 
TSCORE T0004 0 0.00   1CHD - 0 
TSCORE T0004 0 0.00   1GAR B 0 
TSCORE T0004 0 0.00   2HFT - 0 
TSCORE T0004 0 0.00   1YRN A 0 
TSCORE T0004 0 0.00   1BBH A 0 
TSCORE T0004 0 0.00   1KNB - 0 
TSCORE T0004 0 0.00   1CWP A 0 
TSCORE T0004 0 0.00   1CGO - 0 
TSCORE T0004 0 0.00   2MTA C 0 
TSCORE T0004 0 0.00   1PYA A 0 
TSCORE T0004 0 0.00   1BMV 1 0 
TSCORE T0004 0 0.00   1ISU A 0 
TSCORE T0004 0 0.00   1RCB - 0 
TSCORE T0004 0 0.00   1GFF 2 0 
TSCORE T0004 0 0.00   256B A 0 
TSCORE T0004 0 0.00   3SGB I 0 
TSCORE T0004 0 0.00   2SPC A 0 
TSCORE T0004 0 0.00   1MYK A 0 
TSCORE T0004 0 0.00   1IXA - 0 
TSCORE T0004 0 0.00   1SRA - 0 
TSCORE T0004 0 0.00   2TMV P 0 
TSCORE T0004 0 0.00   1BBL - 0 
TSCORE T0004 0 0.00   3HHR B 0 
TSCORE T0004 0 0.00   4MBA - 0 
TSCORE T0004 0 0.00   1ASH - 0 
TSCORE T0004 0 0.00   7API B 0 
TSCORE T0004 0 0.00   1OPR - 0 
TSCORE T0004 0 0.00   1IAA - 0 
TSCORE T0004 0 0.00   1CLG A 0 
TSCORE T0004 0 0.00   2CRD - 0 
TSCORE T0004 0 0.00   2STV - 0 
TSCORE T0004 0 0.00   1PTQ - 0 
TSCORE T0004 0 0.00   1FC2 C 0 
TSCORE T0004 0 0.00   1TSR A 0 
TSCORE T0004 0 0.00   1LIS - 0 
TSCORE T0004 0 0.00   1CUS - 0 
TSCORE T0004 0 0.00   1PRT B 0 
TSCORE T0004 0 0.00   1HCR A 0 
TSCORE T0004 0 0.00   1BBT 1 0 
TSCORE T0004 0 0.00   1BAB A 0 
TSCORE T0004 0 0.00   2ACH B 0 
TSCORE T0004 0 0.00   2MEV 4 0 
TSCORE T0004 0 0.00   2PCD A 0 
TSCORE T0004 0 0.00   1CFB - 0 
TSCORE T0004 0 0.00   1HMP A 0 
TSCORE T0004 0 0.00   1FLP - 0 
TSCORE T0004 0 0.00   1EHS - 0 
TSCORE T0004 0 0.00   1BTD A 0 
TSCORE T0004 0 0.00   1PDC - 0 
TSCORE T0004 0 0.00   1HTR P 0 
TSCORE T0004 0 0.00   1SGT - 0 
TSCORE T0004 0 0.00   1GDI - 0 
TSCORE T0004 0 0.00   1SAC A 0 
TSCORE T0004 0 0.00   2CLG A 0 
TSCORE T0004 0 0.00   1ECO - 0 
TSCORE T0004 0 0.00   1TSS A 0 
TSCORE T0004 0 0.00   1INA - 0 
TSCORE T0004 0 0.00   1PPT - 0 
TSCORE T0004 0 0.00   1FCS - 0 
TSCORE T0004 0 0.00   2BPA 3 0 
TSCORE T0004 0 0.00   1HLB - 0 
TSCORE T0004 0 0.00   9WGA A 0 
TSCORE T0004 0 0.00   4SBV A 0 
TSCORE T0004 0 0.00   1BBA - 0 
TSCORE T0004 0 0.00   3CLA - 0 
TSCORE T0004 0 0.00   1HLE B 0 
TSCORE T0004 0 0.00   1LTS A 0 
TSCORE T0004 0 0.00   1BI6 H 0 
TSCORE T0004 0 0.00   1ILK - 0 
TSCORE T0004 0 0.00   1PVU A 0 
TSCORE T0004 0 0.00   1VCA A 0 
TSCORE T0004 0 0.00   3MDS A 0 
TSCORE T0004 0 0.00   1IAG - 0 
TSCORE T0004 0 0.00   1LE4 - 0 
TSCORE T0004 0 0.00   1ILL G 0 
TSCORE T0004 0 0.00   1FCD C 0 
TSCORE T0004 0 0.00   3GAP A 0 
TSCORE T0004 0 0.00   1TAB I 0 
TSCORE T0004 0 0.00   3SDH A 0 
TSCORE T0004 0 0.00   1DTR - 0 
TSCORE T0004 0 0.00   1BHP - 0 
TSCORE T0004 0 0.00   1GPC - 0 
TSCORE T0004 0 0.00   1UDG - 0 
TSCORE T0004 0 0.00   1HBG - 0 
TSCORE T0004 0 0.00   1ITH A 0 
TSCORE T0004 0 0.00   1PPN - 0 
TSCORE T0004 0 0.00   1BBT 2 0 
TSCORE T0004 0 0.00   1CAG B 0 
TSCORE T0004 0 0.00   1CBN - 0 
TSCORE T0004 0 0.00   1MMO G 0 
TSCORE T0004 0 0.00   1APH B 0 
TSCORE T0004 0 0.00   1PAI B 0 
TSCORE T0004 0 0.00   153L - 0 
TSCORE T0004 0 0.00   1AYH - 0 
TSCORE T0004 0 0.00   1AK3 A 0 
TSCORE T0004 0 0.00   1DBS - 0 
TSCORE T0004 0 0.00   1DFN A 0 
TSCORE T0004 0 0.00   1CPC L 0 
TSCORE T0004 0 0.00   2LIG A 0 
TSCORE T0004 0 0.00   1DMA A 0 
TSCORE T0004 0 0.00   1CPC A 0 
TSCORE T0004 0 0.00   1ILL R 0 
TSCORE T0004 0 0.00   1HUW - 0 
TSCORE T0004 0 0.00   1IFI - 0 
TSCORE T0004 0 0.00   1AEP - 0 
TSCORE T0004 0 0.00   2LAO - 0 
TSCORE T0004 0 0.00   1DMC - 0 
TSCORE T0004 0 0.00   2SCP A 0 
TSCORE T0004 0 0.00   1BGC - 0 
TSCORE T0004 0 0.00   1THV - 0 
TSCORE T0004 0 0.00   1DME - 0 
TSCORE T0004 0 0.00   1HDR - 0 
TSCORE T0004 0 0.00   1LTS C 0 
TSCORE T0004 0 0.00   1REC - 0 
TSCORE T0004 0 0.00   1RCI - 0 
TSCORE T0004 0 0.00   1SE2 - 0 
TSCORE T0004 0 0.00   1PNK A 0 
TSCORE T0004 0 0.00   1MEA - 0 
TSCORE T0004 0 0.00   1BBT 4 0 
TSCORE T0004 0 0.00   1LKI - 0 
TSCORE T0004 0 0.00   1BAM - 0 
TSCORE T0004 0 0.00   1MFA - 0 
TSCORE T0004 0 0.00   1OVI - 0 
TSCORE T0004 0 0.00   1GLQ A 0 
TSCORE T0004 0 0.00   2RN2 - 2
TSCORE T0004 0 0.00   1PVC 3 0 
TSCORE T0004 0 0.00   1NFP - 0 
TSCORE T0004 0 0.00   1PRT A 0 
TSCORE T0004 0 0.00   1CND - 0 
TSCORE T0004 0 0.00   1AHT L 0 
TSCORE T0004 0 0.00   1AHC - 0 
TSCORE T0004 0 0.00   1ILM B 0 
TSCORE T0004 0 0.00   1UBS A 0 
TSCORE T0004 0 0.00   1COS A 0 
TSCORE T0004 0 0.00   1SCS - 0 
TSCORE T0004 0 0.00   1WFB A 0 
TSCORE T0004 0 0.00   3PGM - 0 
TSCORE T0004 0 0.00   1BPB - 0 
TSCORE T0004 0 0.00   1TPF A 0 
TSCORE T0004 0 0.00   1CCO - 0 
TSCORE T0004 0 0.00   2ZTA A 0 
TSCORE T0004 0 0.00   2PCD M 0 
TSCORE T0004 0 0.00   2DNJ A 0 
TSCORE T0004 0 0.00   1LEC - 0 
TSCORE T0004 0 0.00   2MLT A 0 
TSCORE T0004 0 0.00   1LYP - 0 
TSCORE T0004 0 0.00   1ERL - 0 
TSCORE T0004 0 0.00   1GCN - 0 
TSCORE T0004 0 0.00   1STD - 0 
TSCORE T0004 0 0.00   1CAJ - 0 
TSCORE T0004 0 0.00   1BOM B 0 
TSCORE T0004 0 0.00   2TCT - 0 
TSCORE T0004 0 0.00   1HSB A 0 
TSCORE T0004 0 0.00   1PLQ - 0 
TSCORE T0004 0 0.00   1RVE A 0 
TSCORE T0004 0 0.00   1CTM - 0 
TSCORE T0004 0 0.00   1PPE I 0 
TSCORE T0004 0 0.00   1EAF - 0 
TSCORE T0004 0 0.00   1DEA A 0 
TSCORE T0004 0 0.00   1WHT A 0 
TSCORE T0004 0 0.00   1EDT - 0 
TSCORE T0004 0 0.00   1MML - 0 
TSCORE T0004 0 0.00   1APH A 0 
TSCORE T0004 0 0.00   1ABK - 0 
TSCORE T0004 0 0.00   1CSE E 0 
TSCORE T0004 0 0.00   1DRI - 0 
TSCORE T0004 0 0.00   1PYA B 0 
TSCORE T0004 0 0.00   1HDC A 0 
TSCORE T0004 0 0.00   1RLX B 0 
TSCORE T0004 0 0.00   1MMH 6 0 
TSCORE T0004 0 0.00   6RLX A 0 
TSCORE T0004 0 0.00   4BLM A 0 
TSCORE T0004 0 0.00   1MMH 5 0 
TSCORE T0004 0 0.00   1TYS - 0 
TSCORE T0004 0 0.00   6RLX B 0 
TSCORE T0004 0 0.00   2IFO - 0 
TSCORE T0004 0 0.00   1COL A 0 
TSCORE T0004 0 0.00   1ERI A 0 
TSCORE T0004 0 0.00   1CNS A 0 
TSCORE T0004 0 0.00   1HSA A 0 
TSCORE T0004 0 0.00   1NBA A 0 
TSCORE T0004 0 0.00   1RLX A 0 
TSCORE T0004 0 0.00   1MMH 3 0 
TSCORE T0004 0 0.00   1FNB - 0 
TSCORE T0004 0 0.00   1TML - 0 
TSCORE T0004 0 0.00   1BTS - 0 
TSCORE T0004 0 0.00   2AAI B 0 
TSCORE T0004 0 0.00   1MMH 7 0 
TSCORE T0004 0 0.00   1CDL G 0 
TSCORE T0004 0 0.00   1APM I 0 
TSCORE T0004 0 0.00   1MAT - 0 
TSCORE T0004 0 0.00   1GLT - 0 
TSCORE T0004 0 0.00   1CSM A 0 
TSCORE T0004 0 0.00   1SCU A 0 
TSCORE T0004 0 0.00   1ARB - 0 
TSCORE T0004 0 0.00   2SAS - 0 
TSCORE T0004 0 0.00   2PTE E 0 
TSCORE T0004 0 0.00   1BOM A 0 
TSCORE T0004 0 0.00   1CNV - 0 
TSCORE T0004 0 0.00   1RPB - 0 
TSCORE T0004 0 0.00   1ENY - 0 
TSCORE T0004 0 0.00   1LXA - 0 
TSCORE T0004 0 0.00   1THT A 0 
TSCORE T0004 0 0.00   1PRC H 0 
TSCORE T0004 0 0.00   1BTQ - 0 
TSCORE T0004 0 0.00   1NIP B 0 
TSCORE T0004 0 0.00   1HAN - 0 
TSCORE T0004 0 0.00   1BMT A 0 
TSCORE T0004 0 0.00   1DIH - 0 
TSCORE T0004 0 0.00   1ORA - 0 
TSCORE T0004 0 0.00   1IFM - 0 
TSCORE T0004 0 0.00   1SOL - 0 
TSCORE T0004 0 0.00   1PDA - 0 
TSCORE T0004 0 0.00   1EDN - 0 
TSCORE T0004 0 0.00   1DAA A 0 
TSCORE T0004 0 0.00   2MEV 1 0 
TSCORE T0004 0 0.00   2HNP - 0 
TSCORE T0004 0 0.00   1PVC 2 0 
TSCORE T0004 0 0.00   8ABP - 0 
TSCORE T0004 0 0.00   1MMH 4 0 
TSCORE T0004 0 0.00   1MMH 2 0 
TSCORE T0004 0 0.00   1NAR - 0 
TSCORE T0004 0 0.00   1PVC 1 0 
TSCORE T0004 0 0.00   1NAL 1 0 
TSCORE T0004 0 0.00   1BAC - 0 
TSCORE T0004 0 0.00   1MMH 1 0 
TSCORE T0004 0 0.00   1YPT A 0 
TSCORE T0004 0 0.00   1PBN - 0 
TSCORE T0004 0 0.00   1PYP - 0 
TSCORE T0004 0 0.00   1SBP - 0 
TSCORE T0004 0 0.00   3TGL - 0 
TSCORE T0004 0 0.00   1ADS - 0 
TSCORE T0004 0 0.00   1CSN - 0 
TSCORE T0004 0 0.00   1AMB - 0 
TSCORE T0004 0 0.00   1IRK - 0 
TSCORE T0004 0 0.00   2REB - 0 
TSCORE T0004 0 0.00   2DLN - 0 
TSCORE T0004 0 0.00   1AMP - 0 
TSCORE T0004 0 0.00   1PFK A 0 
TSCORE T0004 0 0.00   2PIA - 0 
TSCORE T0004 0 0.00   1TLF A 0 
TSCORE T0004 0 0.00   1FRP A 0 
TSCORE T0004 0 0.00   1EZM - 0 
TSCORE T0004 0 0.00   1BCO - 0 
TSCORE T0004 0 0.00   2HAD - 0 
TSCORE T0004 0 0.00   1CTC - 0 
TSCORE T0004 0 0.00   1MLA - 0 
TSCORE T0004 0 0.00   1GHR - 0 
TSCORE T0004 0 0.00   1XYZ A 0 
TSCORE T0004 0 0.00   3ECA A 0 
TSCORE T0004 0 0.00   1CTT - 0 
TSCORE T0004 0 0.00   2CYP - 0 
TSCORE T0004 0 0.00   1TAH B 0 
TSCORE T0004 0 0.00   1EMD - 0 
TSCORE T0004 0 0.00   1PPK E 0 
TSCORE T0004 0 0.00   1APT - 0 
TSCORE T0004 0 0.00   1ESC - 0 
TSCORE T0004 0 0.00   1QOR A 0 
TSCORE T0004 0 0.00   1BDM A 0 
TSCORE T0004 0 0.00   1BIA - 0 
TSCORE T0004 0 0.00   1PGS - 0 
TSCORE T0004 0 0.00   1PRN - 0 
TSCORE T0004 0 0.00   1PTA - 0 
TSCORE T0004 0 0.00   1TCA - 0 
TSCORE T0004 0 0.00   1GIA - 0 
TSCORE T0004 0 0.00   4TS1 A 0 
TSCORE T0004 0 0.00   2BBV A 0 
TSCORE T0004 0 0.00   1NIF - 0 
TSCORE T0004 0 0.00   1HMY - 0 
TSCORE T0004 0 0.00   2LIV - 0 
TSCORE T0004 0 0.00   1GD1 O 0 
TSCORE T0004 0 0.00   1HGE A 0 
TSCORE T0004 0 0.00   6LDH - 0 
TSCORE T0004 0 0.00   9LDT A 0 
TSCORE T0004 0 0.00   1CEO - 0 
TSCORE T0004 0 0.00   1APM E 0 
TSCORE T0004 0 0.00   1ADD - 0 
TSCORE T0004 0 0.00   2BBK H 0 
TSCORE T0004 0 0.00   1AXN - 0 
TSCORE T0004 0 0.00   1FBA A 0 
TSCORE T0004 0 0.00   1HLE A 0 
TSCORE T0004 0 0.00   2MNR - 0 
TSCORE T0004 0 0.00   3PTE - 0 
TSCORE T0004 0 0.00   1ARP - 0 
TSCORE T0004 0 0.00   1PEA - 0 
TSCORE T0004 0 0.00   2POL A 0 
TSCORE T0004 0 0.00   1OMF - 0 
TSCORE T0004 0 0.00   2NAC A 0 
TSCORE T0004 0 0.00   2BLT A 0 
TSCORE T0004 0 0.00   3BCL - 0 
TSCORE T0004 0 0.00   1HPM - 0 
TSCORE T0004 0 0.00   2OHX A 0 
TSCORE T0004 0 0.00   1OMP - 0 
TSCORE T0004 0 0.00   1PRC C 0 
TSCORE T0004 0 0.00   1CHR A 0 
TSCORE T0004 0 0.00   1BVP 1 0 
TSCORE T0004 0 0.00   1UBS B 0 
TSCORE T0004 0 0.00   1PRC M 0 
TSCORE T0004 0 0.00   1XRA - 0 
TSCORE T0004 0 0.00   2SIL - 0 
TSCORE T0004 0 0.00   1MRR A 0 
TSCORE T0004 0 0.00   1PHP - 0 
TSCORE T0004 0 0.00   1SCU B 0 
TSCORE T0004 0 0.00   1FPS - 0 
TSCORE T0004 0 0.00   1DOB - 0 
TSCORE T0004 0 0.00   1OYB - 0 
TSCORE T0004 0 0.00   7AAT A 0 
TSCORE T0004 0 0.00   1XIC - 0 
TSCORE T0004 0 0.00   1NSC A 0 
TSCORE T0004 0 0.00   1VSG A 0 
TSCORE T0004 0 0.00   1EFT - 0 
TSCORE T0004 0 0.00   4ICD - 0 
TSCORE T0004 0 0.00   1FCD A 0 
TSCORE T0004 0 0.00   1CHM A 0 
TSCORE T0004 0 0.00   1INP - 0 
TSCORE T0004 0 0.00   1AMG - 0 
TSCORE T0004 0 0.00   1PHB - 0 
TSCORE T0004 0 0.00   3MDD A 0 
TSCORE T0004 0 0.00   1ADM A 0 
TSCORE T0004 0 0.00   1TPL A 0 
TSCORE T0004 0 0.00   4ENL - 0 
TSCORE T0004 0 0.00   2DKB - 0 
TSCORE T0004 0 0.00   1GFF 1 0 
TSCORE T0004 0 0.00   1ADE A 0 
TSCORE T0004 0 0.00   1MMO B 0 
TSCORE T0004 0 0.00   1BNC A 0 
TSCORE T0004 0 0.00   1LGR - 0 
TSCORE T0004 0 0.00   1NHP - 0 
TSCORE T0004 0 0.00   1ALK A 0 
TSCORE T0004 0 0.00   1PII - 0 
TSCORE T0004 0 0.00   1CEL A 0 
TSCORE T0004 0 0.00   3GRS - 0 
TSCORE T0004 0 0.00   1GPH 1 0 
TSCORE T0004 0 0.00   1GCB - 0 
TSCORE T0004 0 0.00   5RUB B 0 
TSCORE T0004 0 0.00   1PKY A 0 
TSCORE T0004 0 0.00   2CTS - 0 
TSCORE T0004 0 0.00   1GLK - 0 
TSCORE T0004 0 0.00   1BNH - 0 
TSCORE T0004 0 0.00   1MIN A 0 
TSCORE T0004 0 0.00   1GLN - 0 
TSCORE T0004 0 0.00   1CBG - 0 
TSCORE T0004 0 0.00   1AKL - 0 
TSCORE T0004 0 0.00   2HPD A 0 
TSCORE T0004 0 0.00   1MYP C 0 
TSCORE T0004 0 0.00   1DPG A 0 
TSCORE T0004 0 0.00   1MHL C 0 
TSCORE T0004 0 0.00   1BTC - 0 
TSCORE T0004 0 0.00   1GLA G 0 
TSCORE T0004 0 0.00   1LAM - 0 
TSCORE T0004 0 0.00   1LYL A 0 
TSCORE T0004 0 0.00   1HKG - 0 
TSCORE T0004 0 0.00   1LYL B 0 
TSCORE T0004 0 0.00   1GPM A 0 
TSCORE T0004 0 0.00   1DPP A 0 
TSCORE T0004 0 0.00   1HNY - 0 
TSCORE T0004 0 0.00   3GLY - 0 
TSCORE T0004 0 0.00   8CAT A 0 
TSCORE T0004 0 0.00   3COX - 0 
TSCORE T0004 0 0.00   1OLB A 0 
TSCORE T0004 0 0.00   1SCC - 0 
TSCORE T0004 0 0.00   1PYD A 0 
TSCORE T0004 0 0.00   1OEL A 0 
TSCORE T0004 0 0.00   1DDT - 0 
TSCORE T0004 0 0.00   1CTN - 0 
TSCORE T0004 0 0.00   1THG - 0 
TSCORE T0004 0 0.00   1MMO D 0 
TSCORE T0004 0 0.00   1PNK B 0 
TSCORE T0004 0 0.00   1ASO A 0 
TSCORE T0004 0 0.00   3DPV A 0 
TSCORE T0004 0 0.00   3PMG A 0 
TSCORE T0004 0 0.00   1ECL - 0 
TSCORE T0004 0 0.00   2KAU C 0 
TSCORE T0004 0 0.00   1TSP - 0 
TSCORE T0004 0 0.00   1PTH - 0 
TSCORE T0004 0 0.00   1POX A 0 
TSCORE T0004 0 0.00   3AAH A 0 
TSCORE T0004 0 0.00   1GAL - 0 
TSCORE T0004 0 0.00   1AOR A 0 
TSCORE T0004 0 0.00   1LLA - 0 
TSCORE T0004 0 0.00   1DLC - 0 
TSCORE T0004 0 0.00   1GOF - 0 
TSCORE T0004 0 0.00   1TRK A 0 
TSCORE T0004 0 0.00   1CDG - 0 
TSCORE T0004 0 0.00   1LCF - 0 
TSCORE T0004 0 0.00   1OAC A 0 
TSCORE T0004 0 0.00   1ORD A 0 
TSCORE T0004 0 0.00   8ACN - 0 
TSCORE T0004 0 0.00   1GPB - 0 
TSCORE T0004 0 0.00   1DIK - 0 
TSCORE T0004 0 0.00   1RAE - 0 
TSCORE T0004 0 0.00   1DHX - 0 
REMARK =============================================================
REMARK 
REMARK 
REMARK =============================================================
REMARK Alignment read in,    2 sequences, length is 88
REMARK MSF of bloc file read from standard input 
REMARK bloc2.msf MSF:   88  Type: P today Check: 100 ..
REMARK Name: T0004 Len:   88 Check: 100  Weight: 1.00
REMARK Name: 1ITG  Len:   88 Check: 100  Weight: 1.00
REMARK //
REMARK        1                                                   50
REMARK T0004  AEIEVGRVYT GKVTRIVDFG AFVAIGGGKE GLVHISQIAD KRVEKVTDYL 
REMARK  1ITG  DC.SPG.IWQ LDCTHLEGKV ILVAVHVASG YIEAEVIPAE TGQETAYFLL 
REMARK 
REMARK        51                                      88
REMARK T0004  QMGQEVPVKV LEVDRQGRIR .LSIKEATEQ SQ.P..AA
REMARK  1ITG  KLAGRWPVKT VHTDNGSNFT STTVKAACWW AGIKQEFG
REMARK 
TALIGN T0004 0    1    2 1ITG - 1      55      56     0.60   1 
TALIGN T0004 0    4    6 1ITG - 1      57      59     0.60   1 
TALIGN T0004 0    8   70 1ITG - 1      60     122     0.60   1 
TALIGN T0004 0   71   81 1ITG - 1     124     134     0.60   1 
TALIGN T0004 0   82   82 1ITG - 1     136     136     0.60   1 
TALIGN T0004 0   83   84 1ITG - 1     139     140     0.60   1 
REMARK Alignment read in,    2 sequences, length is 89
REMARK MSF of bloc file read from standard input 
REMARK bloc2.msf MSF:   89  Type: P today Check: 100 ..
REMARK Name: T0004 Len:   89 Check: 100  Weight: 1.00
REMARK Name: 1ITG  Len:   89 Check: 100  Weight: 1.00
REMARK //
REMARK        1                                                   50
REMARK T0004  AEIEVGRVYT GKVTRIVDFG AFVAIGGGKE GLVHISQIAD .KRVEKVTDY 
REMARK  1ITG  DCSPGIWQLD CTHLE.GKVI LVAVHVASGY IEAEVIPAET GQETAYFLLK 
REMARK 
REMARK        51                                       89
REMARK T0004  LQMGQEVPVK VLEVDRQGRI RLSIKEATEQ SQP....AA
REMARK  1ITG  LAGRWPVK.T VHTDNGSNFT .STTVKAACW WAGIKQEFG
REMARK 
TALIGN T0004 0    1   15 1ITG - 1      55      69     0.40   2 
TALIGN T0004 0   17   40 1ITG - 1      70      93     0.40   2 
TALIGN T0004 0   41   57 1ITG - 1      95     111     0.40   2 
TALIGN T0004 0   59   69 1ITG - 1     112     122     0.40   2 
TALIGN T0004 0   71   82 1ITG - 1     123     134     0.40   2 
TALIGN T0004 0   83   84 1ITG - 1     139     140     0.40   2 
REMARK =============================================================
REMARK 
REMARK 


