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= 013841
(435 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JB5|H Chain H, Fab Fragment In Complex With Small Molecule Hapten,
Crystal Form-1
pdb|2JB6|B Chain B, Fab Fragment In Complex With Small Molecule Hapten,
Crystal Form-2
pdb|2JB6|H Chain H, Fab Fragment In Complex With Small Molecule Hapten,
Crystal Form-2
Length = 244
Score = 31.2 bits (69), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 79 YLTVTHLAAEINRRQTITVLALDNSA---MSSLLSKQLSVY-TLRNVLSLHVLTDYFGSK 134
Y + A + R TIT ++A +SSL S+ +VY R +S L+DY+G
Sbjct: 54 YFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARYFMSYKHLSDYWGQG 113
Query: 135 KLHQITNGTALTSSMFQATGSAPGSSG 161
L +++ + S+F S+ +SG
Sbjct: 114 TLVTVSSASTKGPSVFPLAPSSKSTSG 140
>pdb|1WBI|A Chain A, Avr2
pdb|1WBI|B Chain B, Avr2
pdb|1WBI|C Chain C, Avr2
pdb|1WBI|D Chain D, Avr2
pdb|1WBI|E Chain E, Avr2
pdb|1WBI|F Chain F, Avr2
pdb|1WBI|G Chain G, Avr2
pdb|1WBI|H Chain H, Avr2
Length = 129
Score = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 170 GGKVGFGAEDNDGKLDATYVKSVAEFPYNISVLQISQVLNSDEAEAPTP 218
G + GA +++G+ D TY+ +VA+ P NI+ +S +L A P
Sbjct: 18 GSIMTIGAVNDNGEFDGTYITAVADNPGNIT---LSPLLGIQHKRASQP 63
>pdb|2QK4|A Chain A, Human Glycinamide Ribonucleotide Synthetase
pdb|2QK4|B Chain B, Human Glycinamide Ribonucleotide Synthetase
Length = 452
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 256 GGLTVFCPTDAVVNDFMPKYKNLTEAHKVSLLLYHGTP 293
GG+ +CP V ND + K K+ V + GTP
Sbjct: 253 GGMGAYCPAPQVSNDLLLKIKDTVLQRTVDGMQQEGTP 290
>pdb|2FJF|H Chain H, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|B Chain B, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|D Chain D, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|F Chain F, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|I Chain I, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|K Chain K, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|N Chain N, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|P Chain P, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|R Chain R, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|T Chain T, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|V Chain V, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJF|X Chain X, Structure Of The G6 Fab, A Phage Derived Vegf Binding Fab
pdb|2FJG|H Chain H, Structure Of The G6 Fab, A Phage Derived Fab Fragment, In
Complex With Vegf
pdb|2FJG|B Chain B, Structure Of The G6 Fab, A Phage Derived Fab Fragment, In
Complex With Vegf
Length = 227
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 83 THLAAEINRRQTITVLALDNSA---MSSLLSKQLSVY-TLRNVLSLHVLTDYFGSKKLHQ 138
T+ A + R TI+ N+A M+SL ++ +VY R V L DY+G L
Sbjct: 58 TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVT 117
Query: 139 ITNGTALTSSMFQATGSAPGSSG 161
+++ + S+F S+ +SG
Sbjct: 118 VSSASTKGPSVFPLAPSSKSTSG 140
>pdb|3DVN|B Chain B, Crystal Structure Of K63-specific Fab Apu2.16 Bound To
K63-linked Di- Ubiquitin
pdb|3DVN|H Chain H, Crystal Structure Of K63-specific Fab Apu2.16 Bound To
K63-linked Di- Ubiquitin
Length = 230
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 47/106 (44%), Gaps = 5/106 (4%)
Query: 61 HNITRILAKHPEFSTF-NHYLTVTHLAAEINRRQTITVLALDNSA---MSSLLSKQLSVY 116
H + + K E+ + + Y T A + R TI+ N+A M+SL ++ +VY
Sbjct: 38 HWVRQAPGKGLEWVAYISPYYGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVY 97
Query: 117 -TLRNVLSLHVLTDYFGSKKLHQITNGTALTSSMFQATGSAPGSSG 161
R + DY+G L +++ + S+F S+ +SG
Sbjct: 98 YCAREYYRWYTAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSG 143
>pdb|2QQK|H Chain H, Neuropilin-2 A1a2b1b2 Domains In Complex With A
Semaphorin-Blocking Fab
pdb|2QQL|H Chain H, Neuropilin-2 A1a2b1b2 Domains In Complex With A
Semaphorin-Blocking Fab
Length = 231
Score = 29.3 bits (64), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 83 THLAAEINRRQTITVLALDNSA---MSSLLSKQLSVY-----TLRNVLSLHVLTDYFGSK 134
T A + R TI+ N+A M+SL ++ +VY RN L + DY+G
Sbjct: 58 TDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREDFRNRRRLWYVMDYWGQG 117
Query: 135 KLHQITNGTALTSSMFQATGSAPGSSG 161
L +++ + S+F S+ +SG
Sbjct: 118 TLVTVSSASTKGPSVFPLAPSSKSTSG 144
>pdb|1TZI|B Chain B, Crystal Structure Of The Fab Yads2 Complexed With H-Vegf
Length = 222
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 4/87 (4%)
Query: 79 YLTVTHLAAEINRRQTITVLALDNSA---MSSLLSKQLSVYTL-RNVLSLHVLTDYFGSK 134
Y T A + R TI+ N+A M+SL ++ +VY R+ + + DY+G
Sbjct: 54 YAGATAYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRSSYAYYAAMDYWGQG 113
Query: 135 KLHQITNGTALTSSMFQATGSAPGSSG 161
L +++ + S+F S+ +SG
Sbjct: 114 TLVTVSSASTKGPSVFPLAPSSKSTSG 140
>pdb|3DVG|B Chain B, Crystal Structure Of K63-Specific Fab Apu.3a8 Bound To
K63-Linked Di- Ubiquitin
Length = 230
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 46/106 (43%), Gaps = 5/106 (4%)
Query: 61 HNITRILAKHPEFSTF-NHYLTVTHLAAEINRRQTITVLALDNSA---MSSLLSKQLSVY 116
H + + K E+ + Y T A + R TI+ N+A M+SL ++ +VY
Sbjct: 38 HWVRQAPGKGLEWVAYITPYYGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVY 97
Query: 117 -TLRNVLSLHVLTDYFGSKKLHQITNGTALTSSMFQATGSAPGSSG 161
R + DY+G L +++ + S+F S+ +SG
Sbjct: 98 YCAREYYRWYTAIDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSG 143
>pdb|1LQ2|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1 In Complex With Gluco-Phenylimidazole
pdb|1X38|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1 In Complex With Gluco-Phenylimidazole
pdb|1X39|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1 In Complex With Gluco-Phenylimidazole
Length = 602
Score = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 157 PGSSGYVNVTDLKGGKVGFGAEDNDGKLDATYVKSVAEFPYNIS 200
PGS G VTD G GF G+L T+ KSV + P N+
Sbjct: 546 PGSEGQ-GVTDALFGDFGF-----TGRLPRTWFKSVDQLPMNVG 583
>pdb|1EX1|A Chain A, Beta-D-Glucan Exohydrolase From Barley
pdb|1IEX|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1 In Complex With
4i,4iii,4v-S-Trithiocellohexaose
pdb|1IEW|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1 In Complex With
2-Deoxy-2-Fluoro-Alpha-D-Glucoside
pdb|1IEV|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1 In Complex With Cyclohexitol
pdb|1IEQ|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1
pdb|1J8V|A Chain A, Crystal Structure Of Barley Beta-D-Glucan Glucohydrolase
Isoenzyme Exo1 In Complex With 4'-Nitrophenyl
3i-Thiolaminaritrioside
Length = 605
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 157 PGSSGYVNVTDLKGGKVGFGAEDNDGKLDATYVKSVAEFPYNIS 200
PGS G VTD G GF G+L T+ KSV + P N+
Sbjct: 546 PGSEGQ-GVTDALFGDFGF-----TGRLPRTWFKSVDQLPMNVG 583
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
0.316 0.131 0.378
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,687,109
Number of Sequences: 62578
Number of extensions: 365058
Number of successful extensions: 796
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 794
Number of HSP's gapped (non-prelim): 15
length of query: 435
length of database: 14,973,337
effective HSP length: 102
effective length of query: 333
effective length of database: 8,590,381
effective search space: 2860596873
effective search space used: 2860596873
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)