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= 004372
(758 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 = 0.11, Method: Compositional matrix adjust.
Identities = 35/132 (26%), Positives = 56/132 (42%), Gaps = 20/132 (15%)
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 KFKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVHLFDVDIP----NGISFHE 144
Query: 147 RETISKGVDSTS 158
ET+S G ST+
Sbjct: 145 SETLSPGEKSTT 156
>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 = 3.5, 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|1ZCD|A Chain A, Crystal Structure Of The Na+H+ ANTIPORTER NHAA
pdb|1ZCD|B Chain B, Crystal Structure Of The Na+H+ ANTIPORTER NHAA
Length = 388
Score = 29.3 bits (64), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 51/100 (51%), Gaps = 11/100 (11%)
Query: 244 GIHAMFGAFVVGVLVPKEGPFANALVEKVEDL----VSGIFLPLY-FVSSGLKTNIATIQ 298
G+HA +VG +P + + +++E + V+ + LPL+ F ++G+ T+
Sbjct: 223 GVHATLAGVIVGFFIPLKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVTLD 282
Query: 299 GLQSWGLLALVILTACL-GKIVGTFVVSLSFKVPLREALA 337
GL S +L L I+ L GK +G +SL + LR LA
Sbjct: 283 GLTS--ILPLGIIAGLLIGKPLG---ISLFCWLALRLKLA 317
>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 = 9.0, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 618 IVIRFLLAADAIGNTVSVDMAGNASMDEEVLSEFKLKTSRNGS--VRYEERLVRNTAETI 675
I +R L A N + D A +S D + L ++K V+ +RL R+TA+ I
Sbjct: 18 IQVRALKDAGVKANRIFTDKASGSSSDRKGLDLLRMKVKEGDVILVKKLDRLGRDTADMI 77
Query: 676 AVIRE 680
+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
0.323 0.138 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,553,721
Number of Sequences: 62578
Number of extensions: 676201
Number of successful extensions: 1390
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1389
Number of HSP's gapped (non-prelim): 8
length of query: 758
length of database: 14,973,337
effective HSP length: 106
effective length of query: 652
effective length of database: 8,340,069
effective search space: 5437724988
effective search space used: 5437724988
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)