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= 000228
(1825 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 150 bits (379), Expect = 6e-36, Method: Compositional matrix adjust.
Identities = 97/272 (35%), Positives = 150/272 (55%), Gaps = 11/272 (4%)
Query: 594 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQL-PAMVESKISDEAGFGRSLFERLTS 652
++IDE+ Q E E IP+ + G +L+GD QL P ++E K +D AG +SLFERL S
Sbjct: 521 VLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAAD-AGLKQSLFERLIS 578
Query: 653 LNHSKHLLNIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKQYLTGTEFGTYSFINI 712
L H L +QYRM+P +S FP+ FY + +G ++ ++ G
Sbjct: 579 LGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWA 638
Query: 713 IGGREDFIYH--SCRNIVEVSAVIKILQKLYKAWVGSKQKVSIGVVSPYTAQVVAIRKKI 770
GRE+ + S N +E +I+ KL++ V +Q IGV++PY Q I + +
Sbjct: 639 NYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQ---IGVITPYEGQRAYILQYM 695
Query: 771 GFEYE-NKDGFT-VKVKSIDGFQGGEEDIIIISTVRCNTGGSIGFISKPQRVNVALTRAR 828
+KD + V+V S+D FQG E+D II+S VR N +IGF+ P+R+NV LTRA+
Sbjct: 696 QMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAK 755
Query: 829 HCLWILGSERTLISSESIWGALVCDAKARQCF 860
+ L ILG+ R+L + ++W L+ + + C
Sbjct: 756 YGLVILGNPRSL-ARNTLWNHLLIHFREKGCL 786
Score = 54.7 bits (130), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 43/117 (36%), Positives = 64/117 (54%), Gaps = 15/117 (12%)
Query: 251 PSFSSTLNESQVGAMLACLRRLDCGHRSGVELIWGPPGTGKTKTVSMLLLTLLRI-KCRT 309
P+F+ LN SQ A+ L+R + LI GPPGTGKT T + ++ L +I K R
Sbjct: 356 PNFAQ-LNSSQSNAVSHVLQR-------PLSLIQGPPGTGKTVTSATIVYHLSKIHKDRI 407
Query: 310 LACTPTNVAITELASRV----LKLVKESYK--RDSRSNTPICPLGDILLFGNKDRLK 360
L C P+NVA+ LA+++ LK+V+ + K D S+ L +++ G K LK
Sbjct: 408 LVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELK 464
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 149 bits (375), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 93/262 (35%), Positives = 140/262 (53%), Gaps = 9/262 (3%)
Query: 594 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDEAGFGRSLFERLTSL 653
++IDE+ Q E E +P+ L G +L+GD CQL +V K + +AG +SLFERL L
Sbjct: 519 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 577
Query: 654 NHSKHLLNIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKQYLTGTEFGTYSFINII 713
L +QYRMHP++S FP+ FY + +G + + + F +
Sbjct: 578 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 637
Query: 714 GGREDFIYH--SCRNIVEVSAVIKILQKLYKAWVGSKQKVSIGVVSPYTAQVVAIRKKIG 771
G+E+ S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 638 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 694
Query: 772 F--EYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNTGGSIGFISKPQRVNVALTRARH 829
F K V++ S+D FQG E+D II+S VR N IGF++ P+R+NVALTRAR+
Sbjct: 695 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 754
Query: 830 CLWILGSERTLISSESIWGALV 851
+ I+G+ + L S + +W L+
Sbjct: 755 GVIIVGNPKAL-SKQPLWNHLL 775
Score = 50.8 bits (120), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 12/108 (11%)
Query: 242 KGQWDEKFGPSFSSTLNESQVGAMLACLRRLDCGHRSGVELIWGPPGTGKTKTVSMLLLT 301
K Q ++F LN SQV A+ L+R + LI GPPGTGKT T + ++
Sbjct: 342 KCQLPKRFTAQGLPDLNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYH 394
Query: 302 LLRI-KCRTLACTPTNVAITELASRV----LKLVKESYKRDSRSNTPI 344
L R L C P+N+A+ +L ++ LK+V+ K ++P+
Sbjct: 395 LARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPV 442
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 148 bits (373), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 93/262 (35%), Positives = 140/262 (53%), Gaps = 9/262 (3%)
Query: 594 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDEAGFGRSLFERLTSL 653
++IDE+ Q E E +P+ L G +L+GD CQL +V K + +AG +SLFERL L
Sbjct: 342 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 400
Query: 654 NHSKHLLNIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKQYLTGTEFGTYSFINII 713
L +QYRMHP++S FP+ FY + +G + + + F +
Sbjct: 401 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 460
Query: 714 GGREDFIYH--SCRNIVEVSAVIKILQKLYKAWVGSKQKVSIGVVSPYTAQVVAIRKKIG 771
G+E+ S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 461 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 517
Query: 772 F--EYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNTGGSIGFISKPQRVNVALTRARH 829
F K V++ S+D FQG E+D II+S VR N IGF++ P+R+NVALTRAR+
Sbjct: 518 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 577
Query: 830 CLWILGSERTLISSESIWGALV 851
+ I+G+ + L S + +W L+
Sbjct: 578 GVIIVGNPKAL-SKQPLWNHLL 598
Score = 50.8 bits (120), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 12/108 (11%)
Query: 242 KGQWDEKFGPSFSSTLNESQVGAMLACLRRLDCGHRSGVELIWGPPGTGKTKTVSMLLLT 301
K Q ++F LN SQV A+ L+R + LI GPPGTGKT T + ++
Sbjct: 165 KCQLPKRFTAQGLPDLNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYH 217
Query: 302 LLRI-KCRTLACTPTNVAITELASRV----LKLVKESYKRDSRSNTPI 344
L R L C P+N+A+ +L ++ LK+V+ K ++P+
Sbjct: 218 LARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPV 265
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 148 bits (373), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 93/262 (35%), Positives = 140/262 (53%), Gaps = 9/262 (3%)
Query: 594 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDEAGFGRSLFERLTSL 653
++IDE+ Q E E +P+ L G +L+GD CQL +V K + +AG +SLFERL L
Sbjct: 343 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 401
Query: 654 NHSKHLLNIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKQYLTGTEFGTYSFINII 713
L +QYRMHP++S FP+ FY + +G + + + F +
Sbjct: 402 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 461
Query: 714 GGREDFIYH--SCRNIVEVSAVIKILQKLYKAWVGSKQKVSIGVVSPYTAQVVAIRKKIG 771
G+E+ S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 462 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 518
Query: 772 F--EYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNTGGSIGFISKPQRVNVALTRARH 829
F K V++ S+D FQG E+D II+S VR N IGF++ P+R+NVALTRAR+
Sbjct: 519 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 578
Query: 830 CLWILGSERTLISSESIWGALV 851
+ I+G+ + L S + +W L+
Sbjct: 579 GVIIVGNPKAL-SKQPLWNHLL 599
Score = 50.8 bits (120), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 12/108 (11%)
Query: 242 KGQWDEKFGPSFSSTLNESQVGAMLACLRRLDCGHRSGVELIWGPPGTGKTKTVSMLLLT 301
K Q ++F LN SQV A+ L+R + LI GPPGTGKT T + ++
Sbjct: 166 KCQLPKRFTAQGLPDLNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYH 218
Query: 302 LLRI-KCRTLACTPTNVAITELASRV----LKLVKESYKRDSRSNTPI 344
L R L C P+N+A+ +L ++ LK+V+ K ++P+
Sbjct: 219 LARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSREAIDSPV 266
>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 = 104 bits (260), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 85/260 (32%), Positives = 129/260 (49%), Gaps = 23/260 (8%)
Query: 592 NFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDEAGFGRSLFERLT 651
+ +VIDE AQ E+ IPL A +L GD QLP S + AG SL ERL
Sbjct: 368 DVVVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLA 425
Query: 652 SLNHSK--HLLNIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKQYLTGT----EFG 705
++ L +QYRMH +I + + Y Q+ ++V + + L G E G
Sbjct: 426 EEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVAR--HLLRDLPGVAATEETG 483
Query: 706 TYSFINIIGG-----REDFIYHSCRNIVEVSAVIKILQKLYKAWVGSKQKVSIGVVSPYT 760
+ G E+ S N EV V +Q L A V ++ I VVSPY
Sbjct: 484 VPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPAR---DIAVVSPYN 540
Query: 761 AQVVAIRKKIGFEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNTGGSIGFISKPQRV 820
QV +R+ + + +++KS+DGFQG E++ +I+S VR N G +GF+++ +R+
Sbjct: 541 LQVDLLRQSLVHRHPE-----LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 821 NVALTRARHCLWILGSERTL 840
NVA+TRAR + ++ RT+
Sbjct: 596 NVAVTRARRHVAVICDSRTV 615
Score = 50.1 bits (118), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 46/84 (54%), Gaps = 7/84 (8%)
Query: 253 FSSTLNESQVGAMLACLRRLDCGHRSGVELIWGPPGTGKTKTVSMLLLTLLRIKCRTLAC 312
F++ L+ SQ A+L L + + +I GPPGTGKT TV ++L ++ + L C
Sbjct: 186 FNTCLDTSQKEAVLFALSQKELA------IIHGPPGTGKTTTVVEIILQAVKQGLKVLCC 239
Query: 313 TPTNVAITELASRVLKLVKESYKR 336
P+N+A+ L R L L K+ R
Sbjct: 240 APSNIAVDNLVER-LALCKQRILR 262
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 104 bits (260), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 85/260 (32%), Positives = 127/260 (48%), Gaps = 23/260 (8%)
Query: 592 NFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDEAGFGRSLFERLT 651
+ +VIDE AQ E+ IPL A +L GD QLP S + AG SL ERL
Sbjct: 368 DVVVIDECAQALEASCWIPLLKA--RKCILAGDHKQLPPTTVSHKAALAGLSLSLMERLA 425
Query: 652 SLNHSK--HLLNIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKQYLTGT----EFG 705
++ L +QYRMH +I + + Y Q+ ++V L G E G
Sbjct: 426 EEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRD--LPGVAATEETG 483
Query: 706 TYSFINIIGG-----REDFIYHSCRNIVEVSAVIKILQKLYKAWVGSKQKVSIGVVSPYT 760
+ G E+ S N EV V +Q L A V ++ I VVSPY
Sbjct: 484 VPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPAR---DIAVVSPYN 540
Query: 761 AQVVAIRKKIGFEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNTGGSIGFISKPQRV 820
QV +R+ + + +++KS+DGFQG E++ +I+S VR N G +GF+++ +R+
Sbjct: 541 LQVDLLRQSLVHRHPE-----LEIKSVDGFQGREKEAVILSFVRSNRKGEVGFLAEDRRI 595
Query: 821 NVALTRARHCLWILGSERTL 840
NVA+TRAR + ++ RT+
Sbjct: 596 NVAVTRARRHVAVICDSRTV 615
Score = 50.1 bits (118), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 46/84 (54%), Gaps = 7/84 (8%)
Query: 253 FSSTLNESQVGAMLACLRRLDCGHRSGVELIWGPPGTGKTKTVSMLLLTLLRIKCRTLAC 312
F++ L+ SQ A+L L + + +I GPPGTGKT TV ++L ++ + L C
Sbjct: 186 FNTCLDTSQKEAVLFALSQKELA------IIHGPPGTGKTTTVVEIILQAVKQGLKVLCC 239
Query: 313 TPTNVAITELASRVLKLVKESYKR 336
P+N+A+ L R L L K+ R
Sbjct: 240 APSNIAVDNLVER-LALCKQRILR 262
>pdb|3TY3|A Chain A, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe Bound To Glycyl-Glycyl-Glycine
pdb|3TY3|B Chain B, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe Bound To Glycyl-Glycyl-Glycine
pdb|3TY4|A Chain A, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe
pdb|3TY4|B Chain B, Crystal Structure Of Homoisocitrate Dehydrogenase From
Schizosaccharomyces Pombe
Length = 366
Score = 33.9 bits (76), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 8/52 (15%)
Query: 756 VSPYTAQVVAIRKKIGFEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNT 807
V+ Y++ +VA+RKK+G Y N VKS+DG +G D++I VR NT
Sbjct: 90 VAGYSSPIVALRKKMGL-YAN----VRPVKSLDGAKGKPVDLVI---VRENT 133
>pdb|1SXJ|D Chain D, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 353
Score = 32.7 bits (73), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 34/134 (25%), Positives = 52/134 (38%), Gaps = 28/134 (20%)
Query: 245 WDEKFGPSF--SSTLNESQVGAMLACLRRLDCGHRSGVELIWGPPGTGKTKTVSMLLLTL 302
W EK+ P T + V + L+ + H L +GPPGTGKT T+ L L
Sbjct: 27 WVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHM----LFYGPPGTGKTSTILALTKEL 82
Query: 303 LR---IKCRTLACTPTNVAITELASRVLKLVKESYKRDSR-----------SNTPICPLG 348
+K R L ++ R + +V+E K +R N P CP
Sbjct: 83 YGPDLMKSRILELNASD-------ERGISIVREKVKNFARLTVSKPSKHDLENYP-CPPY 134
Query: 349 DILLFGNKDRLKVN 362
I++ D + +
Sbjct: 135 KIIILDEADSMTAD 148
>pdb|3PVS|A Chain A, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|B Chain B, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|C Chain C, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
pdb|3PVS|D Chain D, Structure And Biochemical Activities Of Escherichia Coli
Mgsa
Length = 447
Score = 32.0 bits (71), Expect = 3.6, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 270 RRLDCGHRSGVELIWGPPGTGKT 292
R ++ GH + ++WGPPGTGKT
Sbjct: 43 RAIEAGHLHSM-ILWGPPGTGKT 64
>pdb|3DU5|A Chain A, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3DU5|B Chain B, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3DU6|A Chain A, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3DU6|B Chain B, Structure Of The Catalytic Subunit Of Telomerase, Tert
pdb|3KYL|A Chain A, Structure Of The Catalytic Subunit Of Telomerase Bound To
Its Rna Template And Telomeric Dna
Length = 596
Score = 31.6 bits (70), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 1329 GLYRKVVERCVKDSPWQAFLKCLSQKME 1356
G YRKV +C+K W+AFL L ++ E
Sbjct: 522 GKYRKVTFQCLKSIAWRAFLAVLKRRTE 549
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
0.320 0.135 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 51,540,972
Number of Sequences: 62578
Number of extensions: 2120484
Number of successful extensions: 4691
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 4656
Number of HSP's gapped (non-prelim): 20
length of query: 1825
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1712
effective length of database: 7,902,023
effective search space: 13528263376
effective search space used: 13528263376
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)