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= 004461
(752 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1F89|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Nit3, A
Member Of Branch 10 Of The Nitrilase Superfamily
pdb|1F89|B Chain B, Crystal Structure Of Saccharomyces Cerevisiae Nit3, A
Member Of Branch 10 Of The Nitrilase Superfamily
Length = 291
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 36/138 (26%), Positives = 57/138 (41%), Gaps = 20/138 (14%)
Query: 43 LTRGLAFILRPLR-QPRVIAEITGGILLGPSALGRSERFLQAVFPPKSQTVLDTLANLGL 101
L R FI R ++ QP + P + + ++ + + P + T + L+NL
Sbjct: 29 LQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKYSEVINPKEPSTSVQFLSNLAN 88
Query: 102 IFFMFLVG---LELDPKS---------LRQTGK---KALGIAIAGISLPFALGIGSSFLL 146
F + LVG ELDPK+ + GK K + + + +P G SF
Sbjct: 89 KFKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVHLFDVDIPN----GISFHE 144
Query: 147 RETISKGVDSTSFLVFMG 164
ET+S G ST+ G
Sbjct: 145 SETLSPGEKSTTIDTKYG 162
>pdb|1WXD|A Chain A, Crystal Structure Of Shikimate 5-dehydrogenase (aroe) From
Thermus Thermophilus Hb8
pdb|1WXD|B Chain B, Crystal Structure Of Shikimate 5-dehydrogenase (aroe) From
Thermus Thermophilus Hb8
pdb|2CY0|A Chain A, Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From
Thermus Thermophilus Hb8 In Complex With Nadp
pdb|2CY0|B Chain B, Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From
Thermus Thermophilus Hb8 In Complex With Nadp
pdb|2D5C|A Chain A, Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From
Thermus Thermophilus Hb8 In Complex With Shikimate
pdb|2D5C|B Chain B, Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From
Thermus Thermophilus Hb8 In Complex With Shikimate
pdb|2EV9|A Chain A, Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From
Thermus Thermophilus Hb8 In Complex With Nadp(H) And
Shikimate
pdb|2EV9|B Chain B, Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From
Thermus Thermophilus Hb8 In Complex With Nadp(H) And
Shikimate
Length = 263
Score = 30.4 bits (67), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 88 KSQTVLDTLANLGLIFFMFLVGLELDPKSLRQTGKKALGI 127
K QT L LA G + F GL DP + + ++ALG+
Sbjct: 224 KVQTGLPMLAWQGALAFRLWTGLLPDPSGMEEAARRALGV 263
>pdb|1GHT|A Chain A, Solution Structure Of The Catalytic Domain Of Gamma Delta
Resolvase
pdb|1HX7|A Chain A, Solution Structure Of The Catalytic Domain Of Gamma Delta
Resolvase
Length = 105
Score = 29.3 bits (64), Expect = 7.5, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 612 IVIRFLLAADAIGNTVSVDMAGNASMDEEVLSEFKLKTSRNGS--VRYEERLVRNTAETI 669
I +R L A N + D A +S D + L ++K V+ +RL R+TA+ I
Sbjct: 18 IQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMI 77
Query: 670 AVIRE 674
+I+E
Sbjct: 78 QLIKE 82
>pdb|1GDT|A Chain A, Crystal Structure Of A Site-Specific Recombinase, Gamma-
Delta Resolvase Complexed With A 34 Bp Cleavage Site
pdb|1GDT|B Chain B, Crystal Structure Of A Site-Specific Recombinase, Gamma-
Delta Resolvase Complexed With A 34 Bp Cleavage Site
Length = 183
Score = 29.3 bits (64), Expect = 7.5, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 612 IVIRFLLAADAIGNTVSVDMAGNASMDEEVLSEFKLKTSRNGS--VRYEERLVRNTAETI 669
I +R L A N + D A +S D + L ++K V+ +RL R+TA+ I
Sbjct: 18 IQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMI 77
Query: 670 AVIRE 674
+I+E
Sbjct: 78 QLIKE 82
>pdb|1ZR2|A Chain A, Structure Of A Synaptic Gamma-Delta Resolvase Tetramer
Covalently Linked To Two Cleaved Dnas
pdb|1ZR2|B Chain B, Structure Of A Synaptic Gamma-Delta Resolvase Tetramer
Covalently Linked To Two Cleaved Dnas
pdb|1ZR4|A Chain A, Structure Of A Synaptic Gamma-Delta Resolvase Tetramer
Covalently Linked To Two Cleaved Dnas
pdb|1ZR4|B Chain B, Structure Of A Synaptic Gamma-Delta Resolvase Tetramer
Covalently Linked To Two Cleaved Dnas
pdb|1ZR4|E Chain E, Structure Of A Synaptic Gamma-Delta Resolvase Tetramer
Covalently Linked To Two Cleaved Dnas
pdb|1ZR4|D Chain D, Structure Of A Synaptic Gamma-Delta Resolvase Tetramer
Covalently Linked To Two Cleaved Dnas
Length = 183
Score = 29.3 bits (64), Expect = 7.6, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 612 IVIRFLLAADAIGNTVSVDMAGNASMDEEVLSEFKLKTSRNGS--VRYEERLVRNTAETI 669
I +R L A N + D A +S D + L ++K V+ +RL R+TA+ I
Sbjct: 18 IQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVKEGDVILVKKLDRLGRDTADMI 77
Query: 670 AVIRE 674
+I+E
Sbjct: 78 QLIKE 82
>pdb|2GM4|A Chain A, An Activated, Tetrameric Gamma-Delta Resolvase: Hin
Chimaera Bound To Cleaved Dna
pdb|2GM4|B Chain B, An Activated, Tetrameric Gamma-Delta Resolvase: Hin
Chimaera Bound To Cleaved Dna
Length = 183
Score = 29.3 bits (64), Expect = 8.5, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 612 IVIRFLLAADAIGNTVSVDMAGNASMDEEVLSEFKLKTSRNGS--VRYEERLVRNTAETI 669
I +R L A N + D A +S D + L ++K V+ +RL R+TA+ I
Sbjct: 18 IQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVKEGDVILVKKLDRLGRDTADMI 77
Query: 670 AVIRE 674
+I+E
Sbjct: 78 QLIKE 82
>pdb|2RSL|A Chain A, Refinement Of Gamma Delta Resolvase Reveals A Strikingly
Flexible Molecule
pdb|2RSL|B Chain B, Refinement Of Gamma Delta Resolvase Reveals A Strikingly
Flexible Molecule
pdb|2RSL|C Chain C, Refinement Of Gamma Delta Resolvase Reveals A Strikingly
Flexible Molecule
pdb|1GDR|A Chain A, Model For A Dna Mediated Synaptic Complex Suggested By
Crystal Packing Of Gamma Delta Resolvase Subunits
Length = 140
Score = 29.3 bits (64), Expect = 9.3, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 612 IVIRFLLAADAIGNTVSVDMAGNASMDEEVLSEFKLKTSRNGS--VRYEERLVRNTAETI 669
I +R L A N + D A +S D + L ++K V+ +RL R+TA+ I
Sbjct: 18 IQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVEEGDVILVKKLDRLGRDTADMI 77
Query: 670 AVIRE 674
+I+E
Sbjct: 78 QLIKE 82
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
0.324 0.138 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,173,108
Number of Sequences: 62578
Number of extensions: 651407
Number of successful extensions: 1764
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1763
Number of HSP's gapped (non-prelim): 7
length of query: 752
length of database: 14,973,337
effective HSP length: 106
effective length of query: 646
effective length of database: 8,340,069
effective search space: 5387684574
effective search space used: 5387684574
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.8 bits)