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= psy877
(136 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 63 FTAIKQAELRSSNTSEKNTGALLFTIFRGKISEGIDFADNYARSVISVGIPFP 115
+ I Q EL S + +F + G++SEGI+F N +I G+PFP
Sbjct: 458 YRGIDQKELYSMLKKFRRDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFP 510
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 63 FTAIKQAELRSSNTSEKNTGALLFTIFRGKISEGIDFADNYARSVISVGIPFP 115
+ I Q EL S + +F + G++SEGI+F N +I G+PFP
Sbjct: 476 YRGIDQKELYSMLKKFRRDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFP 528
>pdb|2VL7|A Chain A, Structure Of S. Tokodaii Xpd4
Length = 540
Score = 35.4 bits (80), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 27/42 (64%), Gaps = 2/42 (4%)
Query: 84 LLFTIFRGKISEGIDF--ADNYARSVISVGIPFPSIQDEKVK 123
L+ + R K SEG++F +N S++ G+P+P++ D+ V+
Sbjct: 431 LVMLVMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVR 472
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 32.3 bits (72), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 28/44 (63%), Gaps = 5/44 (11%)
Query: 80 NTGALLFTIFRGKISEGIDFADNYARSVIS----VGIPFPSIQD 119
N L+ ++ +GK++EGI+ +N RS+IS VGIP+P D
Sbjct: 436 NNKVLIGSVGKGKLAEGIELRNN-DRSLISDVVIVGIPYPPPDD 478
>pdb|2ZBK|B Chain B, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|D Chain D, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|F Chain F, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|H Chain H, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
Length = 530
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 34 GLMDRIREVKSVYCEPRRNDELENVMLGYFTAIKQAELRSSNTSEKNTGALLFTIFRGKI 93
LM+ R++K E R+ E + +L Y I + RS T + L + ++ +I
Sbjct: 443 ALMEVARKLKQYLSEKRKEQEAKKKLLAYLKYIPEVS-RSLATFLASGNKELVSKYQNEI 501
Query: 94 SEGI 97
SEG+
Sbjct: 502 SEGL 505
>pdb|4F9I|A Chain A, Crystal Structure Of Proline Utilization A (Puta) From
Geobacter Sulfurreducens Pca
pdb|4F9I|B Chain B, Crystal Structure Of Proline Utilization A (Puta) From
Geobacter Sulfurreducens Pca
Length = 1026
Score = 26.9 bits (58), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 93 ISEGIDFADNYARSVISVGIP 113
++E IDF + YAR +I +G P
Sbjct: 629 VTEAIDFLEYYAREMIRLGQP 649
>pdb|3UXI|A Chain A, Crystal Structure Of L-Rhamnose Isomerase W38a Mutant From
Bacillus Halodurans
pdb|3UXI|B Chain B, Crystal Structure Of L-Rhamnose Isomerase W38a Mutant From
Bacillus Halodurans
pdb|3UXI|C Chain C, Crystal Structure Of L-Rhamnose Isomerase W38a Mutant From
Bacillus Halodurans
pdb|3UXI|D Chain D, Crystal Structure Of L-Rhamnose Isomerase W38a Mutant From
Bacillus Halodurans
Length = 424
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 28 IRWSSTGLMDRIREVKSVYCEPRRNDELENVMLG--YFTA 65
+RW S ++ E++ + E RND L+ V++G +F A
Sbjct: 296 VRWDSDHVVTFDDELREIALEIVRNDALDRVLIGLDFFDA 335
>pdb|3UVA|A Chain A, Crystal Structure Of L-Rhamnose Isomerase Mutant W38f From
Bacillus Halodurans In Complex With Mn
pdb|3UVA|B Chain B, Crystal Structure Of L-Rhamnose Isomerase Mutant W38f From
Bacillus Halodurans In Complex With Mn
pdb|3UVA|C Chain C, Crystal Structure Of L-Rhamnose Isomerase Mutant W38f From
Bacillus Halodurans In Complex With Mn
pdb|3UVA|D Chain D, Crystal Structure Of L-Rhamnose Isomerase Mutant W38f From
Bacillus Halodurans In Complex With Mn
Length = 424
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 28 IRWSSTGLMDRIREVKSVYCEPRRNDELENVMLG--YFTA 65
+RW S ++ E++ + E RND L+ V++G +F A
Sbjct: 296 VRWDSDHVVTFDDELREIALEIVRNDALDRVLIGLDFFDA 335
>pdb|3P14|A Chain A, Crystal Structure Of L-Rhamnose Isomerase With A Novel
High Thermo- Stability From Bacillus Halodurans
pdb|3P14|B Chain B, Crystal Structure Of L-Rhamnose Isomerase With A Novel
High Thermo- Stability From Bacillus Halodurans
pdb|3P14|C Chain C, Crystal Structure Of L-Rhamnose Isomerase With A Novel
High Thermo- Stability From Bacillus Halodurans
pdb|3P14|D Chain D, Crystal Structure Of L-Rhamnose Isomerase With A Novel
High Thermo- Stability From Bacillus Halodurans
pdb|3UU0|A Chain A, Crystal Structure Of L-Rhamnose Isomerase From Bacillus
Halodurans In Complex With Mn
pdb|3UU0|B Chain B, Crystal Structure Of L-Rhamnose Isomerase From Bacillus
Halodurans In Complex With Mn
pdb|3UU0|C Chain C, Crystal Structure Of L-Rhamnose Isomerase From Bacillus
Halodurans In Complex With Mn
pdb|3UU0|D Chain D, Crystal Structure Of L-Rhamnose Isomerase From Bacillus
Halodurans In Complex With Mn
Length = 424
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 28 IRWSSTGLMDRIREVKSVYCEPRRNDELENVMLG--YFTA 65
+RW S ++ E++ + E RND L+ V++G +F A
Sbjct: 296 VRWDSDHVVTFDDELREIALEIVRNDALDRVLIGLDFFDA 335
>pdb|4EAZ|C Chain C, Vgll1-Tead4 Structure
pdb|4EAZ|D Chain D, Vgll1-Tead4 Structure
Length = 60
Score = 26.2 bits (56), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 24/35 (68%), Gaps = 2/35 (5%)
Query: 77 SEKNTGALLFTIFRGKISEGIDFADNYARSVISVG 111
+E N G+++FT F G I+ +D ++++R++ + G
Sbjct: 16 TEWNAGSVIFTYFEGDINSXVD--EHFSRALRNXG 48
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
0.317 0.133 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,951,437
Number of Sequences: 62578
Number of extensions: 143031
Number of successful extensions: 295
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 288
Number of HSP's gapped (non-prelim): 10
length of query: 136
length of database: 14,973,337
effective HSP length: 88
effective length of query: 48
effective length of database: 9,466,473
effective search space: 454390704
effective search space used: 454390704
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: 46 (22.3 bits)