PFRMAT AL 
TARGET T0081 
AUTHOR 7397-8542-2481 
METHOD PSI-BLAST searches did not yield similarities to other protein families, 
METHOD but by performing reverse PSI-BLAST searches on the trailing end hits 
METHOD to MgsA, we found that pyrimidine synthesis protein URA1 as a query  
METHOD sequence hits MgsA. The yeast pyrimidine synthesis protein URA1   
METHOD expanded alignment was used to build an HMM (HMMER 2.0), which 
METHOD found a significant match in the PDB (1jdb - carbamoyl phosphate 
METHOD synthetase).  We used HMMALIGN to add the 1jdb sequence to the alignment, 
METHOD and merged the DSSP assignments for 1jdb and the secondary structure 
METHOD predictions.  We made only very tiny manual adjustments to close some 
METHOD loops. 
MODEL  1 
PARENT 1jdb_B 
H  13    R  943 
I  14    A  944 
A  15    L  945 
L  16    L  946 
V  17    S  947 
A  18    V  948 
H  19    R  949 
D  20    E  950 
H  21    G  951 
C  22    D  952 
K  23    K  953 
Q  24    E  954 
M  25    R  955 
L  26    V  956 
M  27    V  957 
S  28    D  958 
W  29    L  959 
V  30    A  960 
E  31    A  961 
R  32    K  962 
H  33    L  963 
Q  34    L  964 
P  35    K  965 
L  36    Q  966 
Q  39    G  967 
H  40    F  968 
V  41    E  969 
L  42    L  970 
Y  43    D  971 
A  44    A  972 
T  45    T  973 
G  46    H  974 
T  47    G  975 
T  48    T  976 
G  49    A  977 
N  50    I  978 
L  51    V  979 
I  52    L  980 
S  53    G  981 
R  54    E  982 
A  55    A  983 
M  58    I  985 
N  59    N  986 
V  60    P  987 
N  61    R  988 
A  62    L  989 
M  63    V  990 
L  64    N  991 
G  66    K  992 
P  67    V  993 
M  68    H  994 
G  69    E  995 
G  70    G  996 
D  71    R  997 
Q  72    P  998 
Q  73    H   -1 
V  74    I 1000 
G  75    Q 1001 
A  76    D 1002 
L  77    R 1003 
I  78    I 1004 
S  79    K 1005 
E  80    N 1006 
G  81    G 1007 
K  82    E 1008 
I  83    Y 1009 
D  84    T 1010 
V  85    Y 1011 
L  86    I 1012 
I  87    I 1013 
F  88    N 1014 
F  89    T 1015 
W  90    T 1016 
D  91    S 1017 
P  92    G 1018 
L  93    R 1019 
N  94    R 1020 
A  95    A 1021 
V  96    I 1022 
P  97    E 1023 
D 101    D 1024 
V 102    S 1025 
K 103    R 1026 
A 104    V 1027 
L 105    I 1028 
L 106    R 1029 
R 107    R 1030 
L 108    S 1031 
A 109    A 1032 
T 110    L 1033 
V 111    Q 1034 
W 112    Y 1035 
N 113    K 1036 
I 114    V 1037 
P 115    H 1038 
V 116    Y 1039 
A 117    D 1040 
T 118    T 1041 
N 119    T 1042 
V 120    L 1043 
A 121    N 1044 
T 122    G 1045 
A 123    G 1046 
D 124    F 1047 
F 125    A 1048 
I 126    T 1049 
I 127    A 1050 
Q 128    M 1051 
S 129    A 1052 
TER 
END 
