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= psy17045
(211 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QY0|A Chain A, Active Dimeric Structure Of The Catalytic Domain Of C1r
Reveals Enzyme-product Like Contacts
pdb|2QY0|C Chain C, Active Dimeric Structure Of The Catalytic Domain Of C1r
Reveals Enzyme-product Like Contacts
Length = 159
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 113 IQDAGNHLQFALYHIDNVDDGYQFKSSEEVLHTLDNILNCLQRGRTSLIVPRKRTIDDLM 172
IQ+ QF Y I GYQ +VLH+ + C G +PR + I D
Sbjct: 17 IQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAV--CQDDGTWHRAMPRCK-IKDCG 73
Query: 173 KSRNM 177
+ RN+
Sbjct: 74 QPRNL 78
>pdb|1GPZ|A Chain A, The Crystal Structure Of The Zymogen Catalytic Domain Of
Complement Protease C1r
pdb|1GPZ|B Chain B, The Crystal Structure Of The Zymogen Catalytic Domain Of
Complement Protease C1r
Length = 399
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 3/67 (4%)
Query: 113 IQDAGNHLQFALYHIDNVDDGYQFKSSEEVLHTLDNILNCLQRGRTSLIVPRKRTIDDLM 172
IQ+ QF Y I GYQ +VLH+ + C G +PR + I D
Sbjct: 15 IQNLQPQYQFRDYFIATCKQGYQLIEGNQVLHSFTAV--CQDDGTWHRAMPRCK-IKDCG 71
Query: 173 KSRNMKS 179
+ RN+ +
Sbjct: 72 QPRNLPN 78
>pdb|2D7U|A Chain A, Crystal Structure Of Hypothetical Adenylosuccinate
Synthetase, Ph0438 From Pyrococcus Horikoshii Ot3
Length = 339
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 26/44 (59%)
Query: 20 INKEVHIILKQLQTILVECSRRFPLTLFGNEGPYKSDKIILASS 63
+ +E++ L + +LVE ++ F L+L+ PY + K + ASS
Sbjct: 159 VAQEINDALDEGSLVLVEGTQGFGLSLYYGTYPYVTSKDVTASS 202
>pdb|3OJL|A Chain A, Native Structure Of The Udp-N-Acetyl-Mannosamine
Dehydrogenase Cap5o From Staphylococcus Aureus
pdb|3OJL|B Chain B, Native Structure Of The Udp-N-Acetyl-Mannosamine
Dehydrogenase Cap5o From Staphylococcus Aureus
pdb|3OJO|A Chain A, Derivative Structure Of The Udp-N-Acetyl-Mannosamine
Dehydrogenase Cap5o From S. Aureus
pdb|3OJO|B Chain B, Derivative Structure Of The Udp-N-Acetyl-Mannosamine
Dehydrogenase Cap5o From S. Aureus
Length = 431
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 6/49 (12%)
Query: 129 NVDDGYQFKSSEEVLHTLDNILNCLQRGRT----SLIVPRKRTIDDLMK 173
N DD Y+ V+ LD+IL L++G T S I P +T+DD +K
Sbjct: 95 NNDDQYRSCDISLVMRALDSILPFLKKGNTIIVESTIAP--KTMDDFVK 141
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 27.3 bits (59), Expect = 6.0, Method: Composition-based stats.
Identities = 49/207 (23%), Positives = 84/207 (40%), Gaps = 35/207 (16%)
Query: 8 EALCLQKEFEWVINKEVHIILKQLQTILVECSRRFPLTLFGNEGPYKSDKIILASS---- 63
+ L Q E +I E ++ + + ++ R P+T G+E P +S IL+
Sbjct: 555 KKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRF 614
Query: 64 -QDTLKTIVNLNGDSISFADIHLKIHR---HHQHQTQTYKTSILKEHPWKLH--QIQDAG 117
Q+ L V+ +G S+ LK+H+ + + +K +LK+ K ++ A
Sbjct: 615 RQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAAR 674
Query: 118 NHLQFALYHIDNVDDGYQFKSSEEVLHTLDNILNCLQRGRTSLIVPRKRTIDDLMKSRNM 177
L+ D V D EEV+H +LN R T+ L +
Sbjct: 675 RMLERQRDIKDEVWDAL-----EEVIHGKVVLLN------------RAPTLHRL----GI 713
Query: 178 KSLTPPLPEDLAISFYIQSHKLICAAY 204
++ P L E + IQ H L+C A+
Sbjct: 714 QAFQPVLVEGQS----IQLHPLVCEAF 736
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna
Polymerase- Includes Complete Structure With Side-Chains
(Except For Disordered Regions)-Further Refined From
Original Deposition-Contains Additional Sequence
Information
Length = 1265
Score = 27.3 bits (59), Expect = 6.7, Method: Composition-based stats.
Identities = 49/207 (23%), Positives = 84/207 (40%), Gaps = 35/207 (16%)
Query: 8 EALCLQKEFEWVINKEVHIILKQLQTILVECSRRFPLTLFGNEGPYKSDKIILASS---- 63
+ L Q E +I E ++ + + ++ R P+T G+E P +S IL+
Sbjct: 295 KKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRF 354
Query: 64 -QDTLKTIVNLNGDSISFADIHLKIHR---HHQHQTQTYKTSILKEHPWKLH--QIQDAG 117
Q+ L V+ +G S+ LK+H+ + + +K +LK+ K ++ A
Sbjct: 355 RQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAAR 414
Query: 118 NHLQFALYHIDNVDDGYQFKSSEEVLHTLDNILNCLQRGRTSLIVPRKRTIDDLMKSRNM 177
L+ D V D EEV+H +LN R T+ L +
Sbjct: 415 RMLERQRDIKDEVWDAL-----EEVIHGKVVLLN------------RAPTLHRL----GI 453
Query: 178 KSLTPPLPEDLAISFYIQSHKLICAAY 204
++ P L E + IQ H L+C A+
Sbjct: 454 QAFQPVLVEGQS----IQLHPLVCEAF 476
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 27.3 bits (59), Expect = 6.8, Method: Composition-based stats.
Identities = 49/207 (23%), Positives = 84/207 (40%), Gaps = 35/207 (16%)
Query: 8 EALCLQKEFEWVINKEVHIILKQLQTILVECSRRFPLTLFGNEGPYKSDKIILASS---- 63
+ L Q E +I E ++ + + ++ R P+T G+E P +S IL+
Sbjct: 264 KKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRF 323
Query: 64 -QDTLKTIVNLNGDSISFADIHLKIHR---HHQHQTQTYKTSILKEHPWKLH--QIQDAG 117
Q+ L V+ +G S+ LK+H+ + + +K +LK+ K ++ A
Sbjct: 324 RQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAAR 383
Query: 118 NHLQFALYHIDNVDDGYQFKSSEEVLHTLDNILNCLQRGRTSLIVPRKRTIDDLMKSRNM 177
L+ D V D EEV+H +LN R T+ L +
Sbjct: 384 RMLERQRDIKDEVWDAL-----EEVIHGKVVLLN------------RAPTLHRL----GI 422
Query: 178 KSLTPPLPEDLAISFYIQSHKLICAAY 204
++ P L E + IQ H L+C A+
Sbjct: 423 QAFQPVLVEGQS----IQLHPLVCEAF 445
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 26.9 bits (58), Expect = 7.4, Method: Composition-based stats.
Identities = 49/207 (23%), Positives = 84/207 (40%), Gaps = 35/207 (16%)
Query: 8 EALCLQKEFEWVINKEVHIILKQLQTILVECSRRFPLTLFGNEGPYKSDKIILASS---- 63
+ L Q E +I E ++ + + ++ R P+T G+E P +S IL+
Sbjct: 295 KKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRF 354
Query: 64 -QDTLKTIVNLNGDSISFADIHLKIHR---HHQHQTQTYKTSILKEHPWKLH--QIQDAG 117
Q+ L V+ +G S+ LK+H+ + + +K +LK+ K ++ A
Sbjct: 355 RQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAAR 414
Query: 118 NHLQFALYHIDNVDDGYQFKSSEEVLHTLDNILNCLQRGRTSLIVPRKRTIDDLMKSRNM 177
L+ D V D EEV+H +LN R T+ L +
Sbjct: 415 RMLERQRDIKDEVWDAL-----EEVIHGKVVLLN------------RAPTLHRL----GI 453
Query: 178 KSLTPPLPEDLAISFYIQSHKLICAAY 204
++ P L E + IQ H L+C A+
Sbjct: 454 QAFQPVLVEGQS----IQLHPLVCEAF 476
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 0.135 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,194,775
Number of Sequences: 62578
Number of extensions: 245910
Number of successful extensions: 1294
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1292
Number of HSP's gapped (non-prelim): 16
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
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: 49 (23.5 bits)