BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy12057
(172 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WSR|A Chain A, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSR|B Chain B, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSV|A Chain A, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSV|B Chain B, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
Length = 375
Score = 104 bits (259), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 50/109 (45%), Positives = 64/109 (58%)
Query: 61 GKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCP 120
GKRRR FPGA +I Q+K V R+R GL G P+R I N ++G +TSGCP
Sbjct: 265 GKRRRAAMDFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCP 324
Query: 121 SPSLKKNIAMGYIEPAYSKVGVELWXXXXXXXXXXXXTKMPFLKSNYHT 169
SPSLKKN+AMGY+ YS+ G L +KMPF+ +NY+T
Sbjct: 325 SPSLKKNVAMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYT 373
>pdb|3GIR|A Chain A, Crystal Structure Of Glycine Cleavage System
Aminomethyltransferase T From Bartonella Henselae
Length = 393
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 35/107 (32%), Positives = 49/107 (45%), Gaps = 1/107 (0%)
Query: 62 KRRRETGGFPGASIIQSQIKSGVSRKRTGLT-STGVPIRPGYEIFNANDQRVGAITSGCP 120
K RE F GA ++ G SR R GL T PIR G +F+ R+G +TSG
Sbjct: 284 KNVREKAQFYGAKAFLESLQKGPSRCRVGLKPQTRQPIRAGAVLFDNEGNRIGVVTSGGF 343
Query: 121 SPSLKKNIAMGYIEPAYSKVGVELWXXXXXXXXXXXXTKMPFLKSNY 167
PS +AMGY+ A+ G E++ +PF++ Y
Sbjct: 344 GPSFDGPVAMGYVPVAWKVEGTEVFTELRGKKIALSVHSLPFVEQRY 390
>pdb|1YX2|A Chain A, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
pdb|1YX2|B Chain B, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
Length = 365
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/85 (37%), Positives = 50/85 (58%), Gaps = 5/85 (5%)
Query: 59 FPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLT--STGVPIRPGYEIFNANDQRVGAIT 116
F K ++E+ F G S++ Q ++G RK GL G+P R GYE+F N + VG +T
Sbjct: 260 FAVKHKKESD-FFGKSVLSEQKENGAKRKLVGLEXIEKGIP-RHGYEVFQ-NGKSVGKVT 316
Query: 117 SGCPSPSLKKNIAMGYIEPAYSKVG 141
+G SP+L KN+ + I+ S++G
Sbjct: 317 TGTQSPTLGKNVGLALIDSETSEIG 341
>pdb|1V5V|A Chain A, Crystal Structure Of A Component Of Glycine Cleavage
System: T-Protein From Pyrococcus Horikoshii Ot3 At 1.5
A Resolution
pdb|1V5V|B Chain B, Crystal Structure Of A Component Of Glycine Cleavage
System: T-Protein From Pyrococcus Horikoshii Ot3 At 1.5
A Resolution
Length = 401
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 70 FPGASIIQSQIKSGVSRK--RTGLTSTGVPIRPGYEIFNANDQRVGAITSGCPSPSLKKN 127
F G + Q + GV RK + G+P R GY+++ AN + +G +TSG SP L
Sbjct: 297 FIGKDALLKQKERGVGRKLVHFKMIDKGIP-REGYKVY-ANGEMIGEVTSGTLSPLLNVG 354
Query: 128 IAMGYIEPAYSKVGVEL 144
I + +++ Y+K G+E+
Sbjct: 355 IGIAFVKEEYAKPGIEI 371
>pdb|1WOO|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOP|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOR|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOS|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
Length = 364
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 3/67 (4%)
Query: 79 QIKSGVSRKRTGLTSTGVPI-RPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAY 137
+ K V RK L +G I R GYE+ N +RVG ITSG SP+L K+IA+ + +
Sbjct: 272 KAKEKVERKLVALELSGKRIARKGYEVLK-NGERVGEITSGNFSPTLGKSIALALVSKSV 330
Query: 138 SKVGVEL 144
K+G +L
Sbjct: 331 -KIGDQL 336
>pdb|3K8D|A Chain A, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8D|B Chain B, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8D|C Chain C, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8D|D Chain D, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase In Complex With Ctp And 2-Deoxy-Kdo
pdb|3K8E|C Chain C, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
pdb|3K8E|D Chain D, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
pdb|3K8E|A Chain A, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
pdb|3K8E|B Chain B, Crystal Structure Of E. Coli Lipopolysaccharide Specific
Cmp-Kdo Synthetase
Length = 264
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 73 ASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRV 112
A+II+ Q+ +++++ G+ + VPI E FN N +V
Sbjct: 122 ATIIR-QVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKV 160
>pdb|3TTG|A Chain A, Crystal Structure Of Putative Aminomethyltransferase From
Leptospirillum Rubarum
Length = 355
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 75 IIQSQIKSGVSRKRTGLTSTGVPIRPGYE----IFNAND-QRVGAITSGCPSPSLKKNIA 129
+ + + + ++R G G P P E +FN D G +T S L I
Sbjct: 266 VTRLKFQGHLNRSLAGFRLEGGPF-PKXEFPVTLFNPKDGNEAGILTRTSSSDILGSGIG 324
Query: 130 MGYIEPAYSKVGVEL 144
+GYI+ +S+ G EL
Sbjct: 325 LGYIKRNFSENGTEL 339
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.136 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,756,425
Number of Sequences: 62578
Number of extensions: 163001
Number of successful extensions: 274
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 269
Number of HSP's gapped (non-prelim): 7
length of query: 172
length of database: 14,973,337
effective HSP length: 92
effective length of query: 80
effective length of database: 9,216,161
effective search space: 737292880
effective search space used: 737292880
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)