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= psy11433
(941 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/137 (24%), Positives = 63/137 (45%), Gaps = 28/137 (20%)
Query: 57 ITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEA 116
+ KLK+ G + CPY+ ++ A ++ +Y Y + + +L R ++V DEA
Sbjct: 124 VKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDL-REYMIVIDEA 182
Query: 117 HNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQ 176
HN+D V E+++ I T++ +K+ K +S ++ ++L+ LR+
Sbjct: 183 HNLDKV----------NELEERSLSEI-TIQMAIKQSKSEESRRI---LSKLLNQLREV- 227
Query: 177 SARETDVVLANPVLPDE 193
VLPDE
Sbjct: 228 ------------VLPDE 232
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/137 (24%), Positives = 63/137 (45%), Gaps = 28/137 (20%)
Query: 712 ITKLKEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSSVVVFDEA 771
+ KLK+ G + CPY+ ++ A ++ +Y Y + + +L R ++V DEA
Sbjct: 124 VKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDL-REYMIVIDEA 182
Query: 772 HNIDNVCVDSLSVRINRRTIEKAVGNIQTLEGTLKEMKEADSAKLREEYARLVEGLRDAQ 831
HN+D V E+++ I T++ +K+ K +S ++ ++L+ LR+
Sbjct: 183 HNLDKV----------NELEERSLSEI-TIQMAIKQSKSEESRRI---LSKLLNQLREV- 227
Query: 832 SARETDVVLANPVLPDE 848
VLPDE
Sbjct: 228 ------------VLPDE 232
>pdb|2VL7|A Chain A, Structure Of S. Tokodaii Xpd4
Length = 540
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 78/179 (43%), Gaps = 27/179 (15%)
Query: 637 LQKRKLLFIETQDALDSRSVSKERDGKIVDGRCHSLTSSSVRDRHKAGE------NIPVC 690
L+K+ L+F T LDS ++ K++ + L S + G+ N C
Sbjct: 50 LKKKVLIFTRTHSQLDSIY----KNAKLLGLKTGFLIGKSASCIYAQGDEEPDEINCSKC 105
Query: 691 DFYEKFDAVGREAPLAPGVYSITKL-KEMGRELGLCPYFLARQAIIHAKIVVYSYHYLLD 749
+K + + P +KL +E + CPY+ R + ++ +Y YL
Sbjct: 106 RLKDKIKTIEDKEP--------SKLIEEFKDAVDYCPYYSLRANLKDKDVIAMTYPYLFQ 157
Query: 750 PKIANVV--SKE---LARSSVVVFDEAHNIDNVCVDSLSVR-INRRTIEKAVGNIQTLE 802
I N V +K+ ++V DEAHN+ + D R I+R+ +E+A+ I+ +E
Sbjct: 158 KPIRNSVFCNKDDCLKLEDYLIVIDEAHNL--LEADKWFTRKISRKMLERALKEIEIVE 214
Score = 35.4 bits (80), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 70 CPYFLARQAIIHAKIVVYSYHYLLDPKIANVV--SKE---LARSSVVVFDEAHNIDNVCV 124
CPY+ R + ++ +Y YL I N V +K+ ++V DEAHN+ +
Sbjct: 133 CPYYSLRANLKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNL--LEA 190
Query: 125 DSLSVR-INRRTIEKAVGNIQTLE 147
D R I+R+ +E+A+ I+ +E
Sbjct: 191 DKWFTRKISRKMLERALKEIEIVE 214
Score = 32.0 bits (71), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 10/80 (12%)
Query: 628 WYDQGIIDNLQKRKLLFIETQDALDSRSVSKERD---------GKIV-DGRCHSLTSSSV 677
W+ + I + +R L IE + L+ K +D K++ DGRCH L+ +
Sbjct: 193 WFTRKISRKMLERALKEIEIVERLNRIDAKKVKDYINLLIDYMSKLIKDGRCHELSLMPL 252
Query: 678 RDRHKAGENIPVCDFYEKFD 697
DR GE I V Y D
Sbjct: 253 PDRETNGELIVVTRAYLNID 272
Score = 29.3 bits (64), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 17/34 (50%)
Query: 9 IVDGRCHSLTSSSVRDRHKAGENIPVCDFYEKFD 42
I DGRCH L+ + DR GE I V Y D
Sbjct: 239 IKDGRCHELSLMPLPDRETNGELIVVTRAYLNID 272
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 62 EMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSS---VVVFDEAHN 118
+ G +CPY + A+ A IV+ Y Y L+ +A S V++ DEAHN
Sbjct: 138 DYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHN 197
Query: 119 IDNVCVDSLSVRINRRTIEKA 139
+ ++ S RI+ ++ +A
Sbjct: 198 LPDIGRSIGSFRISVESLNRA 218
Score = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 717 EMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSS---VVVFDEAHN 773
+ G +CPY + A+ A IV+ Y Y L+ +A S V++ DEAHN
Sbjct: 138 DYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHN 197
Query: 774 IDNVCVDSLSVRINRRTIEKA 794
+ ++ S RI+ ++ +A
Sbjct: 198 LPDIGRSIGSFRISVESLNRA 218
Score = 37.0 bits (84), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 463 LEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELARLFDYYIKHNE 522
LE P+G+GKT L + Y + L K+LY RT + E+V++EL L +
Sbjct: 9 LESPTGSGKTIMALKSALQYSSERKL---KVLYLVRTNSQEEQVIKELRSL-------SS 58
Query: 523 EINMTGLVLSSRKNLCI 539
+ + + + R N+CI
Sbjct: 59 TMKIRAIPMQGRVNMCI 75
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 62 EMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSS---VVVFDEAHN 118
+ G +CPY + A+ A IV+ Y Y L+ +A S V++ DEAHN
Sbjct: 156 DYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHN 215
Query: 119 IDNVCVDSLSVRINRRTIEKA 139
+ ++ S RI+ ++ +A
Sbjct: 216 LPDIGRSIGSFRISVESLNRA 236
Score = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 717 EMGRELGLCPYFLARQAIIHAKIVVYSYHYLLDPKIANVVSKELARSS---VVVFDEAHN 773
+ G +CPY + A+ A IV+ Y Y L+ +A S V++ DEAHN
Sbjct: 156 DYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHN 215
Query: 774 IDNVCVDSLSVRINRRTIEKA 794
+ ++ S RI+ ++ +A
Sbjct: 216 LPDIGRSIGSFRISVESLNRA 236
Score = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 30/101 (29%), Positives = 47/101 (46%), Gaps = 14/101 (13%)
Query: 443 EQYAYMVE----LKKALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSR 498
E Y VE L+ +L LE P+G+GKT L + Y + L K+LY R
Sbjct: 3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKL---KVLYLVR 59
Query: 499 TVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCI 539
T + E+V++EL L + + + + + R N+CI
Sbjct: 60 TNSQEEQVIKELRSL-------SSTMKIRAIPMQGRVNMCI 93
>pdb|1QHB|A Chain A, Vanadium Bromoperoxidase From Red Alga Corallina
Officinalis
pdb|1QHB|B Chain B, Vanadium Bromoperoxidase From Red Alga Corallina
Officinalis
pdb|1QHB|C Chain C, Vanadium Bromoperoxidase From Red Alga Corallina
Officinalis
pdb|1QHB|D Chain D, Vanadium Bromoperoxidase From Red Alga Corallina
Officinalis
pdb|1QHB|E Chain E, Vanadium Bromoperoxidase From Red Alga Corallina
Officinalis
pdb|1QHB|F Chain F, Vanadium Bromoperoxidase From Red Alga Corallina
Officinalis
Length = 596
Score = 35.8 bits (81), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 2/97 (2%)
Query: 493 LLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLVLSSRKNLCIHSEFETRDDISVI 552
L PE++ +VEEL+ + D NE+ N+ +S K+ + F
Sbjct: 421 FLKSESVFPEVDVLVEELSSILDDSASSNEKQNIADGDVSPGKSFLLPMAFAEGSPFHPS 480
Query: 553 RNYGQLLVDIACVVPDGVVCFFTSYLYLESVFETRDD 589
G +V ACV + FF + ++ VFE D
Sbjct: 481 YGSGHAVVAGACVTI--LKAFFDANFQIDQVFEVDTD 515
>pdb|1AVC|A Chain A, Bovine Annexin Vi (Calcium-Bound)
Length = 673
Score = 31.2 bits (69), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/38 (26%), Positives = 25/38 (65%)
Query: 493 LLYCSRTVPEIEKVVEELARLFDYYIKHNEEINMTGLV 530
++ C+R+ P++ +V +E ++ +Y ++H + M+G V
Sbjct: 549 MILCTRSYPDLRRVFQEFVKMTNYDVEHTIKKEMSGDV 586
>pdb|2HNG|A Chain A, The Crystal Structure Of Protein Of Unknown Function
Sp1558 From Streptococcus Pneumoniae
Length = 127
Score = 31.2 bits (69), Expect = 3.1, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 366 LAIKPVFDRFQTVVITSGTLSPLD-MYPKILNFQPVIMHSFSMTLARPCLLPMVRENYAM 424
L+ VFD+F + SGT+S ++ + +I+N + TLARPCL + R Y +
Sbjct: 58 LSFXIVFDKF----VISGTISQVNHIDGRIVNEPSELNQEEVETLARPCLNXLNRLTYEV 113
Query: 425 GLMIDDLP 432
+ DLP
Sbjct: 114 TEIALDLP 121
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 29.6 bits (65), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 454 ALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELA 511
AL K ++ P GTGKTT+++ +I+ + K+L C+ + ++ +VE LA
Sbjct: 201 ALSQKELAIIHGPPGTGKTTTVVEIILQAVKQG----LKVLCCAPSNIAVDNLVERLA 254
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 29.6 bits (65), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 454 ALDAKGHCLLEMPSGTGKTTSLLSLIVAYMNAHPLDVTKLLYCSRTVPEIEKVVEELA 511
AL K ++ P GTGKTT+++ +I+ + K+L C+ + ++ +VE LA
Sbjct: 201 ALSQKELAIIHGPPGTGKTTTVVEIILQAVKQG----LKVLCCAPSNIAVDNLVERLA 254
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
0.321 0.137 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,504,015
Number of Sequences: 62578
Number of extensions: 1043372
Number of successful extensions: 2592
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2568
Number of HSP's gapped (non-prelim): 32
length of query: 941
length of database: 14,973,337
effective HSP length: 108
effective length of query: 833
effective length of database: 8,214,913
effective search space: 6843022529
effective search space used: 6843022529
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)