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= 048652
(1382 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 153 bits (387), Expect = 5e-37, Method: Compositional matrix adjust.
Identities = 98/278 (35%), Positives = 151/278 (54%), Gaps = 11/278 (3%)
Query: 587 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQL-PAMVESKISDGASFGRSLFERLTL 645
++IDE+ Q E E IP+ + G +L+GD QL P ++E K +D A +SLFERL
Sbjct: 521 VLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAAD-AGLKQSLFERLIS 578
Query: 646 LNHSKHLLDIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTEFGPYTFINI 705
L H L++QYRM+P +S FP+ FY + +G ++ ++ P G
Sbjct: 579 LGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWA 638
Query: 706 IGGREEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQMVSIGVVSPYTAQVVAIRK-- 761
GREE + S N +E +I+ KL++ V +Q IGV++PY Q I +
Sbjct: 639 NYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQ---IGVITPYEGQRAYILQYM 695
Query: 762 KIGSEYENKDGFTVKVKSVDGFQGGEEDIIIISTVRCNTGGSIGFISNPQRVNVALTRAR 821
++ + V+V SVD FQG E+D II+S VR N +IGF+ +P+R+NV LTRA+
Sbjct: 696 QMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAK 755
Query: 822 HCLWILGNERTLISSESIWGTLVCDAKARQCFFKADED 859
+ L ILGN R+L + ++W L+ + + C + D
Sbjct: 756 YGLVILGNPRSL-ARNTLWNHLLIHFREKGCLVEGTLD 792
Score = 50.4 bits (119), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 38/113 (33%), Positives = 59/113 (52%), Gaps = 14/113 (12%)
Query: 248 STLNEPQVGAVFACLRRLDCDHKSGVELRWGPPGTGKTKTVSMLLFSLLRI-KCRTLACT 306
+ LN Q AV L+R + L GPPGTGKT T + +++ L +I K R L C
Sbjct: 359 AQLNSSQSNAVSHVLQR-------PLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCA 411
Query: 307 PTNVAITELASR----ALRLVKESYK--RDSRNNTPFCPLGDILLFGNKDRLK 353
P+NVA+ LA++ L++V+ + K D ++ L +++ G K LK
Sbjct: 412 PSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELK 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 = 150 bits (378), Expect = 7e-36, Method: Compositional matrix adjust.
Identities = 94/262 (35%), Positives = 139/262 (53%), Gaps = 9/262 (3%)
Query: 587 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDGASFGRSLFERLTLL 646
++IDE+ Q E E +P+ L G +L+GD CQL +V K + A +SLFERL +L
Sbjct: 519 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 577
Query: 647 NHSKHLLDIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTEFGPYTFINII 706
L +QYRMHP++S FP+ FY + +G + + + F +
Sbjct: 578 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 637
Query: 707 GGREEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQMVSIGVVSPYTAQVVAIRK--K 762
G+EE S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 638 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 694
Query: 763 IGSEYENKDGFTVKVKSVDGFQGGEEDIIIISTVRCNTGGSIGFISNPQRVNVALTRARH 822
K V++ SVD FQG E+D II+S VR N IGF+++P+R+NVALTRAR+
Sbjct: 695 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 754
Query: 823 CLWILGNERTLISSESIWGTLV 844
+ I+GN + L S + +W L+
Sbjct: 755 GVIIVGNPKAL-SKQPLWNHLL 775
Score = 43.9 bits (102), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 12/92 (13%)
Query: 250 LNEPQVGAVFACLRRLDCDHKSGVELRWGPPGTGKTKTVSMLLFSLLRI-KCRTLACTPT 308
LN QV AV L+R + L GPPGTGKT T + +++ L R L C P+
Sbjct: 357 LNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 409
Query: 309 NVAITELASR----ALRLVKESYKRDSRNNTP 336
N+A+ +L + L++V+ K ++P
Sbjct: 410 NIAVDQLTEKIHQTGLKVVRLCAKSREAIDSP 441
>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 = 149 bits (377), Expect = 9e-36, Method: Compositional matrix adjust.
Identities = 94/262 (35%), Positives = 139/262 (53%), Gaps = 9/262 (3%)
Query: 587 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDGASFGRSLFERLTLL 646
++IDE+ Q E E +P+ L G +L+GD CQL +V K + A +SLFERL +L
Sbjct: 343 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 401
Query: 647 NHSKHLLDIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTEFGPYTFINII 706
L +QYRMHP++S FP+ FY + +G + + + F +
Sbjct: 402 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 461
Query: 707 GGREEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQMVSIGVVSPYTAQVVAIRK--K 762
G+EE S N E + V KI KL KA Q IG+++PY Q + + +
Sbjct: 462 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 518
Query: 763 IGSEYENKDGFTVKVKSVDGFQGGEEDIIIISTVRCNTGGSIGFISNPQRVNVALTRARH 822
K V++ SVD FQG E+D II+S VR N IGF+++P+R+NVALTRAR+
Sbjct: 519 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 578
Query: 823 CLWILGNERTLISSESIWGTLV 844
+ I+GN + L S + +W L+
Sbjct: 579 GVIIVGNPKAL-SKQPLWNHLL 599
Score = 44.3 bits (103), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 250 LNEPQVGAVFACLRRLDCDHKSGVELRWGPPGTGKTKTVSMLLFSLLRI-KCRTLACTPT 308
LN QV AV L+R + L GPPGTGKT T + +++ L R L C P+
Sbjct: 181 LNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 233
Query: 309 NVAITELASR 318
N+A+ +L +
Sbjct: 234 NIAVDQLTEK 243
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 149 bits (376), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 97/263 (36%), Positives = 142/263 (53%), Gaps = 11/263 (4%)
Query: 587 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVESKISDGASFGRSLFERLTLL 646
++IDE+ Q E E +P+ L G +L+GD CQL +V K + A +SLFERL +L
Sbjct: 342 ILIDESTQATEPECMVPVVL-GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVL 400
Query: 647 NHSKHLLDIQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTEFGPYTFINII 706
L +QYRMHP++S FP+ FY + +G + + + F +
Sbjct: 401 GIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVT 460
Query: 707 GGREEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQMVSIGVVSPYTAQ---VVAIRK 761
G+EE S N E + V KI KL KA Q IG+++PY Q +V +
Sbjct: 461 QGQEEIASSGTSYLNRTEAANVEKITTKLLKAGAKPDQ---IGIITPYEGQRSYLVQYMQ 517
Query: 762 KIGSEYENKDGFTVKVKSVDGFQGGEEDIIIISTVRCNTGGSIGFISNPQRVNVALTRAR 821
GS + K V++ SVD FQG E+D II+S VR N IGF+++P+R+NVALTRAR
Sbjct: 518 FSGSLH-TKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRAR 576
Query: 822 HCLWILGNERTLISSESIWGTLV 844
+ + I+GN + L S + +W L+
Sbjct: 577 YGVIIVGNPKAL-SKQPLWNHLL 598
Score = 44.3 bits (103), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 8/70 (11%)
Query: 250 LNEPQVGAVFACLRRLDCDHKSGVELRWGPPGTGKTKTVSMLLFSLLRI-KCRTLACTPT 308
LN QV AV L+R + L GPPGTGKT T + +++ L R L C P+
Sbjct: 180 LNHSQVYAVKTVLQR-------PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS 232
Query: 309 NVAITELASR 318
N+A+ +L +
Sbjct: 233 NIAVDQLTEK 242
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 110 bits (276), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 95/296 (32%), Positives = 147/296 (49%), Gaps = 27/296 (9%)
Query: 563 ASLFFSTASSSYKLHSVKIEP---LNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDEC 619
A++ +T + + +K+ P + +VIDE AQ E+ IPL A +L GD
Sbjct: 343 ANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA--RKCILAGDHK 400
Query: 620 QLPAMVESKISDGASFGRSLFERLTLLNHSK--HLLDIQYRMHPSISLFPNLQFYRNQIL 677
QLP S + A SL ERL ++ L +QYRMH +I + + Y Q+
Sbjct: 401 QLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLT 460
Query: 678 DGANVKSKSYEKHYLPGT----EFG-PYTFINIIG----GREEFIYHSCRNMVEVSVVIK 728
++V LPG E G P ++ G EE S N EV +V
Sbjct: 461 AHSSVARHLLRD--LPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSL 518
Query: 729 ILQKLYKAWVGSKQMVSIGVVSPYTAQVVAIRKKIGSEYENKDGFTVKVKSVDGFQGGEE 788
+Q L A V ++ I VVSPY QV +R+ + + +++KSVDGFQG E+
Sbjct: 519 HIQALVDAGVPAR---DIAVVSPYNLQVDLLRQSLVHRHPE-----LEIKSVDGFQGREK 570
Query: 789 DIIIISTVRCNTGGSIGFISNPQRVNVALTRARHCLWILGNERTLISSESIWGTLV 844
+ +I+S VR N G +GF++ +R+NVA+TRAR + ++ + RT +++ + TLV
Sbjct: 571 EAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRT-VNNHAFLKTLV 625
Score = 44.3 bits (103), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 278 GPPGTGKTKTVSMLLFSLLRIKCRTLACTPTNVAITELASRALRLVKESYKR 329
GPPGTGKT TV ++ ++ + L C P+N+A+ L R L L K+ R
Sbjct: 212 GPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVER-LALCKQRILR 262
>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 = 110 bits (276), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 95/296 (32%), Positives = 147/296 (49%), Gaps = 27/296 (9%)
Query: 563 ASLFFSTASSSYKLHSVKIEP---LNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDEC 619
A++ +T + + +K+ P + +VIDE AQ E+ IPL A +L GD
Sbjct: 343 ANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLLKA--RKCILAGDHK 400
Query: 620 QLPAMVESKISDGASFGRSLFERLTLLNHSK--HLLDIQYRMHPSISLFPNLQFYRNQIL 677
QLP S + A SL ERL ++ L +QYRMH +I + + Y Q+
Sbjct: 401 QLPPTTVSHKAALAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLT 460
Query: 678 DGANVKSKSYEKHYLPGT----EFG-PYTFINIIG----GREEFIYHSCRNMVEVSVVIK 728
++V LPG E G P ++ G EE S N EV +V
Sbjct: 461 AHSSVARHLLRD--LPGVAATEETGVPLLLVDTAGCGLFELEEEDEQSKGNPGEVRLVSL 518
Query: 729 ILQKLYKAWVGSKQMVSIGVVSPYTAQVVAIRKKIGSEYENKDGFTVKVKSVDGFQGGEE 788
+Q L A V ++ I VVSPY QV +R+ + + +++KSVDGFQG E+
Sbjct: 519 HIQALVDAGVPAR---DIAVVSPYNLQVDLLRQSLVHRHPE-----LEIKSVDGFQGREK 570
Query: 789 DIIIISTVRCNTGGSIGFISNPQRVNVALTRARHCLWILGNERTLISSESIWGTLV 844
+ +I+S VR N G +GF++ +R+NVA+TRAR + ++ + RT +++ + TLV
Sbjct: 571 EAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRT-VNNHAFLKTLV 625
Score = 44.3 bits (103), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 25/41 (60%)
Query: 278 GPPGTGKTKTVSMLLFSLLRIKCRTLACTPTNVAITELASR 318
GPPGTGKT TV ++ ++ + L C P+N+A+ L R
Sbjct: 212 GPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAVDNLVER 252
>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 = 33.5 bits (75), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 43/182 (23%), Positives = 72/182 (39%), Gaps = 42/182 (23%)
Query: 238 WDEKFGPSL--SSTLNEPQVGAVFACLRRLDCDHKSGVELRWGPPGTGKTKTVSML---L 292
W EK+ P T + V + L+ + H L +GPPGTGKT T+ L L
Sbjct: 27 WVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHM----LFYGPPGTGKTSTILALTKEL 82
Query: 293 FSLLRIKCRTLACTPTNVAITELASRALRLVKESYKRDSR-----------NNTPFCPLG 341
+ +K R L ++ R + +V+E K +R N P CP
Sbjct: 83 YGPDLMKSRILELNASD-------ERGISIVREKVKNFARLTVSKPSKHDLENYP-CPPY 134
Query: 342 DILLFGNKDRLKVNPGFEEIYLDYRVKRLMECFAPLSGWRHCF-----SSMIDLLEDCVS 396
I++ D + + ++R ME ++ ++ R C + +ID L S
Sbjct: 135 KIIILDEADSMTADA-------QSALRRTMETYSGVT--RFCLICNYVTRIIDPLASQCS 185
Query: 397 QY 398
++
Sbjct: 186 KF 187
>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 = 32.0 bits (71), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 8/52 (15%)
Query: 749 VSPYTAQVVAIRKKIGSEYENKDGFTVKVKSVDGFQGGEEDIIIISTVRCNT 800
V+ Y++ +VA+RKK+G Y N VKS+DG +G D++I VR NT
Sbjct: 90 VAGYSSPIVALRKKMGL-YAN----VRPVKSLDGAKGKPVDLVI---VRENT 133
>pdb|1SXJ|C Chain C, Crystal Structure Of The Eukaryotic Clamp Loader
(Replication Factor C, Rfc) Bound To The Dna Sliding
Clamp (Proliferating Cell Nuclear Antigen, Pcna)
Length = 340
Score = 32.0 bits (71), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 238 WDEKFGPSLSSTLNEP-QVGAVFACLRRLDCDHKSGVELRWGPPGTGKTKTVSML 291
W EK+ P TL+E V +R+ + K L +GPPGTGKT T+ L
Sbjct: 15 WVEKYRPE---TLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVAL 66
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 0.135 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 39,545,778
Number of Sequences: 62578
Number of extensions: 1620033
Number of successful extensions: 3896
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 3862
Number of HSP's gapped (non-prelim): 21
length of query: 1382
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1271
effective length of database: 8,027,179
effective search space: 10202544509
effective search space used: 10202544509
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: 58 (26.9 bits)