PFRMAT AL
TARGET T0348 NESG:CvR39, Chromobacterium violaceum (ATCC 12472), 68 res
AUTHOR SAM-T99
REMARK Subject: T0348(database hits)
REMARK MIME-Version: 1.0
REMARK Content-type: multipart/mixed; Boundary="simple mime boundary"
REMARK 
REMARK --simple mime boundary
REMARK Content-type: text/plain; charset=us-ascii
REMARK 
REMARK The following are search results using the SAM-T99 method
REMARK for a sequence query against a database. If there
REMARK are no hits associated with this output, then your
REMARK score cutoff was too conservative.
REMARK 
REMARK Citation:  
REMARK   K. Karplus, C. Barrett, and R. Hughey,
REMARK   Hidden Markov Models for Detecting Remote Protein Homologies,
REMARK   Bioinformatics, 1998, vol. 14, no. 10, pp. 846-856. 
REMARK   http://www.cse.ucsc.edu/research/compbio/HMM-apps
REMARK --------------------------------------------------------
REMARK 
REMARK For questions or problems, please see the SAM-T99 FAQ at
REMARK 
REMARK http://www.cse.ucsc.edu/research/compbio/HMM-apps/sam-t99-faq.html
REMARK 
REMARK or email us at sam-info@cse.ucsc.edu
REMARK 
REMARK 
REMARK --simple mime boundary
REMARK Content-type: text/plain; charset=us-ascii; name='t99-results-1151429785-28112.t99dbhits.txt'
REMARK Content-Disposition: attachment; filename="t99-results-1151429785-28112.t99dbhits.txt"
REMARK 
REMARK The E-value is an estimate of approximately  how many
REMARK sequences would score this well by chance in the database
REMARK searched.  For SAM-T99, E-values less than about 0.01 are
REMARK roughly equivalent, as sequences that score that well have
REMARK most likely already been included in the SAM-T99 multiple
REMARK alignment.
REMARK 
REMARK Database: PDB (updated Thu Jun 22 01:13:09 2006)
REMARK Score method: average
REMARK 
REMARK Summary of Database Hits:
REMARK                   Average               Target               Template     
REMARK SeqID       Reverse     EValue    Reverse     EValue    Reverse     EValue  SeqLabel
REMARK 1pft         -12.19     0.4182     -12.19      0.419  ---------  ---------  :mol:protein length:50  TFIIB                      
REMARK 
REMARK 
REMARK --simple mime boundary
REMARK Content-type: text/plain; charset=us-ascii; name='t99-results-1151429785-28112.t99pairwise.casp.al'
REMARK Content-Disposition: attachment; filename="t99-results-1151429785-28112.t99pairwise.casp.al"
REMARK 
REMARK 
REMARK 
METHOD This pairwise alignment was produced using the SAM-T99 method
METHOD 
METHOD  ------------- Citations (SAM, SAM-T99, HMMs) -----------------
METHOD R. Hughey, A. Krogh, Hidden Markov models for sequence analysis:
METHOD   Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
METHOD K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting
METHOD   remote protein homologies, Bioinformatics 14(10):846-856, 1999.
METHOD A. Krogh et al., Hidden Markov models in computational biology:
METHOD   Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
METHOD -------------
MODEL 1
PARENT 1pft
V 10    V 7
C 11    C 8
P 12    P 9
L 13    A 10
C 14    C 11
K 15    S 13
G 16    A 14
P 17    E 15
L 18    L 16
V 19    I 17
F 20    Y 18
D 21    D 19
K 22    P 20
S 23    E 21
K 24    R 22
D 25    G 23
E 26    E 24
L 27    I 25
I 28    V 26
C 29    C 27
K 30    A 28
G 31    K 29
D 32    C 30
R 33    G 31
F 36    Y 32
P 37    V 33
I 38    I 34
K 39    E 35
D 40    E 36
G 41    N 37
I 42    I 38
P 43    I 39
M 44    D 40
M 45    M 41
L 46    G 42
E 47    P 43
S 48    E 44
TER
END