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= 048135
(1189 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 40.0 bits (92), Expect = 0.009, Method: Composition-based stats.
Identities = 55/221 (24%), Positives = 90/221 (40%), Gaps = 12/221 (5%)
Query: 529 LSLKSYHIIELPNSIGRLMHLRYLDMSNTAISSLPESTCSLINLQTLLLRRCFYLMKWPS 588
L L+S + + P+ RL HL++ + + LP++ L+TL L R L P+
Sbjct: 86 LELRSVPLPQFPDQAFRLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLARN-PLRALPA 144
Query: 589 KVMNLINLRHLDITDVHLIKEMPLGMEEWKCLQTLSNFIVSEGLENATDLQDPTKAILSD 648
+ +L LR L I + E+P + L + +GL N L+ I S
Sbjct: 145 SIASLNRLRELSIRACPELTELP------EPLASTDASGEHQGLVNLQSLRLEWTGIRSL 198
Query: 649 KNDLECLVLECRYPFRAYSQSVLGMLKSH-TSLKELTIK-CYGGTRFPSWVGDPSFSNIV 706
+ L R S LG H L+EL ++ C +P G + +
Sbjct: 199 PASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFG--GRAPLK 256
Query: 707 MITLESCTNCRSLP-SLGLLCSLKALTIREMTELKIIGSEI 746
+ L+ C+N +LP + L L+ L +R L + S I
Sbjct: 257 RLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLI 297
Score = 38.9 bits (89), Expect = 0.017, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 46/98 (46%)
Query: 526 LRVLSLKSYHIIELPNSIGRLMHLRYLDMSNTAISSLPESTCSLINLQTLLLRRCFYLMK 585
L+ L L+ I LP SI L +L+ L + N+ +S+L + L L+ L LR C L
Sbjct: 185 LQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRN 244
Query: 586 WPSKVMNLINLRHLDITDVHLIKEMPLGMEEWKCLQTL 623
+P L+ L + D + +PL + L+ L
Sbjct: 245 YPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKL 282
Score = 32.7 bits (73), Expect = 1.2, Method: Composition-based stats.
Identities = 25/111 (22%), Positives = 53/111 (47%), Gaps = 10/111 (9%)
Query: 522 KFKKLRVLSLKSYHIIELPNSIGRLMHLRYLDMSNTAISSLPESTCSLINLQTLLLRRCF 581
+ L+ ++ + + ELP++ + L L ++ + +LP S SL L+ L +R C
Sbjct: 102 RLSHLQHXTIDAAGLXELPDTXQQFAGLETLTLARNPLRALPASIASLNRLRELSIRACP 161
Query: 582 YLMKWPSKVMN---------LINLRHLDITDVHLIKEMPLGMEEWKCLQTL 623
L + P + + L+NL+ L + + I+ +P + + L++L
Sbjct: 162 ELTELPEPLASTDASGEHQGLVNLQSLRL-EWTGIRSLPASIANLQNLKSL 211
Score = 31.6 bits (70), Expect = 3.0, Method: Composition-based stats.
Identities = 33/126 (26%), Positives = 55/126 (43%), Gaps = 10/126 (7%)
Query: 823 SFASLPVLSDLSIDGCKGL------VCESFQKVEYLKVVRCEELIYLWQNEIWLEKTPIR 876
S ASL L +LSI C L + + E+ +V + L W + P
Sbjct: 145 SIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTG---IRSLPAS 201
Query: 877 LHGLTSPKKLCIENCQRLVSFQEVCFLPILGELEIKNCSALKFLPEGMKHNNVCLECLLI 936
+ L + K L I N + LP L EL+++ C+AL+ P + L+ L++
Sbjct: 202 IANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPP-IFGGRAPLKRLIL 260
Query: 937 EGCNSL 942
+ C++L
Sbjct: 261 KDCSNL 266
Score = 31.2 bits (69), Expect = 3.7, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 34/60 (56%), Gaps = 5/60 (8%)
Query: 1014 NLECLHQIYIWDCSSFTSFPK---GGLPNTLSRISIGKCENLVALPDRMHNLSSLQELEI 1070
+L L ++ + C++ ++P G P L R+ + C NL+ LP +H L+ L++L++
Sbjct: 227 HLPKLEELDLRGCTALRNYPPIFGGRAP--LKRLILKDCSNLLTLPLDIHRLTQLEKLDL 284
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 33.5 bits (75), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 512 SNMFLSDLLPKFKKLRVLSLKSYHIIELPNSIGRLMHLRYLDMSNTAISSLPESTCSLIN 571
+N+F D L + L L + ELP I L +LR LD+S+ ++SLP S
Sbjct: 241 ANIFKYDFLTR------LYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQ 294
Query: 572 LQTLLLRRCFYLMKWPSKVMNLINLRHLDITDVHLIKEM 610
L+ + P + NL NL+ L + L K+
Sbjct: 295 LKYFYFFDNM-VTTLPWEFGNLCNLQFLGVEGNPLEKQF 332
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 500 MLKGDHTCARFISNMFLSDLLPKFKKL---RVLSLKSYHIIELPNSIGRLMHLRYLDMSN 556
+ K D +++ L++L + K L RVL L + LP +G L+Y +
Sbjct: 243 IFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFD 302
Query: 557 TAISSLPESTCSLINLQTL 575
+++LP +L NLQ L
Sbjct: 303 NMVTTLPWEFGNLCNLQFL 321
>pdb|2CVF|A Chain A, Crystal Structure Of The Radb Recombinase
pdb|2CVF|B Chain B, Crystal Structure Of The Radb Recombinase
pdb|2CVH|A Chain A, Crystal Structure Of The Radb Recombinase
pdb|2CVH|B Chain B, Crystal Structure Of The Radb Recombinase
Length = 220
Score = 31.2 bits (69), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 11/87 (12%)
Query: 151 GKTTLA---------RLVYNDKEVEGFNPKAWVCVSEDFDVLKITKAILESVTSSPSNLK 201
GKTTLA ++ Y D E GF+P+ V ++E L +A+ + +PS+ K
Sbjct: 32 GKTTLALQTGLLSGKKVAYVDTE-GGFSPERLVQMAETRG-LNPEEALSRFILFTPSDFK 89
Query: 202 DLNQVQIQLEKAIAGQKFLIVLDNVWS 228
+ +V L+K + L+V+D++ +
Sbjct: 90 EQRRVIGSLKKTVDSNFALVVVDSITA 116
>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
Gorgonarius In Complex With Hypoxanthine-Containing Dna
Length = 773
Score = 30.4 bits (67), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 41/139 (29%), Positives = 61/139 (43%), Gaps = 18/139 (12%)
Query: 349 DILPVLRLSYHHLPSHLKRCFSYSAIF--PKGYEFEEMELILLW-MADGLIQQS----ED 401
D+ PV+R + + LP++ Y AIF PK + E E+ W +GL + + ED
Sbjct: 259 DLYPVIRRTIN-LPTYTLEAV-YEAIFGQPKEKVYAE-EIAQAWETGEGLERVARYSMED 315
Query: 402 NKQMEDLGHKYF--RDLLSRSIFQKSCNNSSKFLMHDLVNDLAQWVSGETNFRLEDELKA 459
K +LG ++F LSR + Q + S +L +W + +EL
Sbjct: 316 AKVTYELGKEFFPMEAQLSRLVGQSLWDVS-----RSSTGNLVEWFLLRKAYE-RNELAP 369
Query: 460 NKQPERFRRARHSSYVCGY 478
NK ER R SY GY
Sbjct: 370 NKPDERELARRRESYAGGY 388
>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
Gorgonarius
Length = 773
Score = 30.4 bits (67), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 41/139 (29%), Positives = 61/139 (43%), Gaps = 18/139 (12%)
Query: 349 DILPVLRLSYHHLPSHLKRCFSYSAIF--PKGYEFEEMELILLW-MADGLIQQS----ED 401
D+ PV+R + + LP++ Y AIF PK + E E+ W +GL + + ED
Sbjct: 259 DLYPVIRRTIN-LPTYTLEAV-YEAIFGQPKEKVYAE-EIAQAWETGEGLERVARYSMED 315
Query: 402 NKQMEDLGHKYF--RDLLSRSIFQKSCNNSSKFLMHDLVNDLAQWVSGETNFRLEDELKA 459
K +LG ++F LSR + Q + S +L +W + +EL
Sbjct: 316 AKVTYELGKEFFPMEAQLSRLVGQSLWDVS-----RSSTGNLVEWFLLRKAYE-RNELAP 369
Query: 460 NKQPERFRRARHSSYVCGY 478
NK ER R SY GY
Sbjct: 370 NKPDERELARRRESYAGGY 388
>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography. V93q Polymerase Variant
Length = 773
Score = 30.4 bits (67), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 41/139 (29%), Positives = 61/139 (43%), Gaps = 18/139 (12%)
Query: 349 DILPVLRLSYHHLPSHLKRCFSYSAIF--PKGYEFEEMELILLW-MADGLIQQS----ED 401
D+ PV+R + + LP++ Y AIF PK + E E+ W +GL + + ED
Sbjct: 259 DLYPVIRRTIN-LPTYTLEAV-YEAIFGQPKEKVYAE-EIAQAWETGEGLERVARYSMED 315
Query: 402 NKQMEDLGHKYF--RDLLSRSIFQKSCNNSSKFLMHDLVNDLAQWVSGETNFRLEDELKA 459
K +LG ++F LSR + Q + S +L +W + +EL
Sbjct: 316 AKVTYELGKEFFPMEAQLSRLVGQSLWDVS-----RSSTGNLVEWFLLRKAYE-RNELAP 369
Query: 460 NKQPERFRRARHSSYVCGY 478
NK ER R SY GY
Sbjct: 370 NKPDERELARRRESYAGGY 388
>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
X-Ray Crystallography
Length = 773
Score = 30.4 bits (67), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 41/139 (29%), Positives = 61/139 (43%), Gaps = 18/139 (12%)
Query: 349 DILPVLRLSYHHLPSHLKRCFSYSAIF--PKGYEFEEMELILLW-MADGLIQQS----ED 401
D+ PV+R + + LP++ Y AIF PK + E E+ W +GL + + ED
Sbjct: 259 DLYPVIRRTIN-LPTYTLEAV-YEAIFGQPKEKVYAE-EIAQAWETGEGLERVARYSMED 315
Query: 402 NKQMEDLGHKYF--RDLLSRSIFQKSCNNSSKFLMHDLVNDLAQWVSGETNFRLEDELKA 459
K +LG ++F LSR + Q + S +L +W + +EL
Sbjct: 316 AKVTYELGKEFFPMEAQLSRLVGQSLWDVS-----RSSTGNLVEWFLLRKAYE-RNELAP 369
Query: 460 NKQPERFRRARHSSYVCGY 478
NK ER R SY GY
Sbjct: 370 NKPDERELARRRESYAGGY 388
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
0.322 0.138 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,495,258
Number of Sequences: 62578
Number of extensions: 1466944
Number of successful extensions: 3120
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 3100
Number of HSP's gapped (non-prelim): 24
length of query: 1189
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1079
effective length of database: 8,089,757
effective search space: 8728847803
effective search space used: 8728847803
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: 57 (26.6 bits)