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= 002254
(947 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J5W|A Chain A, Crystal Structure Of Glycyl-Trna Synthetase Alpha Chain
(Tm0216) From Thermotoga Maritima At 1.95 A Resolution
pdb|1J5W|B Chain B, Crystal Structure Of Glycyl-Trna Synthetase Alpha Chain
(Tm0216) From Thermotoga Maritima At 1.95 A Resolution
Length = 298
Score = 286 bits (733), Expect = 3e-77, Method: Compositional matrix adjust.
Identities = 129/234 (55%), Positives = 175/234 (74%)
Query: 2 YVEPSIRPDDSRYGENPNRLQRHTQFQVILKPDPGNSQDLFIRSLSALGIDVTEHDIRFV 61
YV+PS RP D RYGENPNRLQR+ Q+QVI+KP P NSQ+L++ SL LGI++ EHDIRFV
Sbjct: 64 YVQPSRRPTDGRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFV 123
Query: 62 EDNWESPVLGAWGLGWEIWMDGMEITQFTYFQQAGSLQLSPVSVEITYGLERILMLLQGV 121
EDNWESP LGAWG+GWE+W+DG EITQFTYFQQ G + L + +EITYGLERI LQGV
Sbjct: 124 EDNWESPTLGAWGVGWEVWLDGXEITQFTYFQQIGGISLKDIPLEITYGLERIAXYLQGV 183
Query: 122 DHFKKIQYADGITYGELFLENEKEMSAYYLEHANVHHLQKQFDFFEEESRSLLASGLAIP 181
D+ ++Q+ + + YG++FLENE+E S + E ANV L + FD +E+E L+ L +P
Sbjct: 184 DNVYEVQWNENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLYLP 243
Query: 182 AYDQLLKTSHAFNILDSRGFVGVTERARYFGRMRSLARQCAQLWLKTRKSLGHP 235
AYD +LK SH FN+LD+RG + V++R Y R+++ AR+ A+++L+ + + P
Sbjct: 244 AYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAXARKAARVFLEVQANENSP 297
>pdb|3RF1|A Chain A, The Crystal Structure Of Glycyl-Trna Synthetase Subunit
Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc 11168
pdb|3RF1|B Chain B, The Crystal Structure Of Glycyl-Trna Synthetase Subunit
Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc 11168
pdb|3RGL|A Chain A, The Crystal Structure Of Glycyl-Trna Synthetase Subunit
Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc In
Complex With Atp And Glycine
pdb|3RGL|B Chain B, The Crystal Structure Of Glycyl-Trna Synthetase Subunit
Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc In
Complex With Atp And Glycine
pdb|3UFG|A Chain A, The Crystal Structure Of Glycyl-Trna Synthetase Subunit
Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc In
Complex With Atp
pdb|3UFG|B Chain B, The Crystal Structure Of Glycyl-Trna Synthetase Subunit
Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc In
Complex With Atp
Length = 311
Score = 251 bits (641), Expect = 1e-66, Method: Compositional matrix adjust.
Identities = 117/231 (50%), Positives = 159/231 (68%), Gaps = 4/231 (1%)
Query: 2 YVEPSIRPDDSRYGENPNRLQRHTQFQVILKPDPGNSQDLFIRSLSALGIDVTEHDIRFV 61
YV PS RP D RYGENPNRL + QFQV++KP P N Q+L+++SL LG D+ HDIRFV
Sbjct: 76 YVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFV 135
Query: 62 EDNWESPVLGAWGLGWEIWMDGMEITQFTYFQQAGSLQLSPVSVEITYGLERILMLLQGV 121
EDNWESP LGAWGLGWE+W+DG E+TQFTYFQQ G + + VS EITYGLERI LQ V
Sbjct: 136 EDNWESPSLGAWGLGWEVWLDGXEVTQFTYFQQVGGIAVDLVSAEITYGLERIAXYLQNV 195
Query: 122 DHFKKIQYA----DGITYGELFLENEKEMSAYYLEHANVHHLQKQFDFFEEESRSLLASG 177
D+ I ++ + I Y ++ ++E E S Y E ++V L +QF+ +E +++L G
Sbjct: 196 DNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQG 255
Query: 178 LAIPAYDQLLKTSHAFNILDSRGFVGVTERARYFGRMRSLARQCAQLWLKT 228
LA+PAYD +H FN+LD+RG + V +R Y ++R L++ CA+++ K
Sbjct: 256 LALPAYDYCXLAAHTFNLLDARGAISVAQRQDYXLKIRELSKNCAEIYKKN 306
>pdb|3SP1|A Chain A, Crystal Structure Of Cysteinyl-Trna Synthetase (Cyss) From
Borrelia Burgdorferi
pdb|3SP1|B Chain B, Crystal Structure Of Cysteinyl-Trna Synthetase (Cyss) From
Borrelia Burgdorferi
Length = 501
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 27/123 (21%), Positives = 46/123 (37%), Gaps = 8/123 (6%)
Query: 40 DLFIRSLSALGIDVTEHDIRFVEDNWESPVLGAWGLGWEIWMDGMEITQFTYFQQAGSLQ 99
D F R+ + + T + E W+SP WG G+ W YF+ A +
Sbjct: 202 DKFKRNKTDFVLWFTNSKFKDQEMKWDSP----WGFGYPSWHLECAAMNLEYFKDALDIH 257
Query: 100 LSPVSVEITYGLERILMLLQGVDHFKKIQYADGITYGELFLENEKEMSAYYLEHANVHHL 159
L V + + I + + F ++ D +GE + + +MS V L
Sbjct: 258 LGGVDHIGVHHINEIAI----AECFLNKKWCDVFVHGEFLIMDYNKMSKSRGNFITVKDL 313
Query: 160 QKQ 162
+ Q
Sbjct: 314 EDQ 316
>pdb|1FDJ|A Chain A, Fructose 1,6-Bisphosphate Aldolase From Rabbit Liver
pdb|1FDJ|B Chain B, Fructose 1,6-Bisphosphate Aldolase From Rabbit Liver
pdb|1FDJ|C Chain C, Fructose 1,6-Bisphosphate Aldolase From Rabbit Liver
pdb|1FDJ|D Chain D, Fructose 1,6-Bisphosphate Aldolase From Rabbit Liver
Length = 363
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 18/71 (25%)
Query: 438 GVLSGNLSYGLRNTPLATVKVQNAESYAGVMRNAGVKIKIEDRRK---TIFDRSNALAKS 494
G+L+ + S G L +KV+N+E E+RR+ +F N++ +S
Sbjct: 28 GILAADESVGTMGNRLQRIKVENSE---------------ENRRQFREILFTVDNSINQS 72
Query: 495 VNGRIIFEESL 505
+ G I+F E+L
Sbjct: 73 IGGVILFHETL 83
>pdb|3QOK|A Chain A, Crystal Structure Of Putative Chitinase Ii From Klebsiella
Pneumoniae
Length = 420
Score = 30.0 bits (66), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 38 SQDLFIRSLSALGIDVTEHDIRFVEDNWESPVLGAWGL 75
S+ +FIRS + + ++ + ++ +WE PV GAWGL
Sbjct: 131 SRAVFIRSAQKI---IQQYGLDGIDLDWEFPVNGAWGL 165
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
0.320 0.136 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,205,888
Number of Sequences: 62578
Number of extensions: 1058621
Number of successful extensions: 2747
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2744
Number of HSP's gapped (non-prelim): 7
length of query: 947
length of database: 14,973,337
effective HSP length: 108
effective length of query: 839
effective length of database: 8,214,913
effective search space: 6892312007
effective search space used: 6892312007
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)