RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12660
(294 letters)
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 101 bits (252), Expect = 3e-24
Identities = 38/145 (26%), Positives = 66/145 (45%), Gaps = 13/145 (8%)
Query: 27 EDFNGVGESEPNPYFYQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVIN 86
E+ G S Y N EA + + G +I I++ Y GQ+ + +
Sbjct: 465 EEIASSGTS------YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQ 518
Query: 87 TRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAMSRARL 143
+ + + + ++ +VD +QG++ D+I+LS VR +G L D RRL VA++RAR
Sbjct: 519 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 578
Query: 144 GLYVFARVSLFRNCFELTPAFNQLM 168
G+ + P +N L+
Sbjct: 579 GVIIVGNPKALSKQ----PLWNHLL 599
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 95.8 bits (238), Expect = 3e-22
Identities = 38/145 (26%), Positives = 66/145 (45%), Gaps = 13/145 (8%)
Query: 27 EDFNGVGESEPNPYFYQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVIN 86
E+ G S Y N EA + + G +I I++ Y GQ+ + +
Sbjct: 641 EEIASSGTS------YLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQ 694
Query: 87 TRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAMSRARL 143
+ + + + ++ +VD +QG++ D+I+LS VR +G L D RRL VA++RAR
Sbjct: 695 FSGSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARY 754
Query: 144 GLYVFARVSLFRNCFELTPAFNQLM 168
G+ + P +N L+
Sbjct: 755 GVIIVGNPKALSKQ----PLWNHLL 775
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 93.1 bits (231), Expect = 2e-21
Identities = 37/134 (27%), Positives = 63/134 (47%), Gaps = 9/134 (6%)
Query: 27 EDFNGVGESEPNPYFYQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVIN 86
E+ + G S + N EA C + + G +I +++ Y GQ+ I +
Sbjct: 643 EEISANGTS------FLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQ 696
Query: 87 TRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAMSRARL 143
+ + + +V +VD +QG++ DYI+LS VR ++G LRD RRL V ++RA+
Sbjct: 697 MNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKY 756
Query: 144 GLYVFARVSLFRNC 157
GL +
Sbjct: 757 GLVILGNPRSLARN 770
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 40.8 bits (95), Expect = 5e-04
Identities = 42/261 (16%), Positives = 79/261 (30%), Gaps = 87/261 (33%)
Query: 10 YQKANAGLVYDFQLINVEDFNGVGESEPNPYFYQNLAEAEYCVALFMYMRLLGYPAHKIT 69
++ G + QL+ + F G G ++ YF E +R L Y
Sbjct: 146 FRAVGEG---NAQLVAI--FGGQGNTDD--YF------EE--------LRDL-Y------ 177
Query: 70 ILSTYNGQKHLIRDVINTRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVRTASVGHLR 129
TY L+ D+I + L +K Q + +L + S
Sbjct: 178 --QTY---HVLVGDLIKF--SAETLSELIRTTLDAEKVFTQGLN--ILEWLENPSNTP-- 226
Query: 130 DVRRLI-VAMSRARLGLYVFARVSLFRNCFELTP-------------------------- 162
D L+ + +S +G+ A + TP
Sbjct: 227 DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET 286
Query: 163 ----AFNQLMIRPQQL--HI--VPHETFPTSRLNTSRVPNSVAIQDMV--HMTTLVYNFY 212
+F + + + I +E +P + L S + +S+ + V M L
Sbjct: 287 DSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPM--LS---- 340
Query: 213 MDKVNGMKKEFYSK--AKLNA 231
++ + +E K N+
Sbjct: 341 ---ISNLTQEQVQDYVNKTNS 358
Score = 36.2 bits (83), Expect = 0.015
Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 33/95 (34%)
Query: 218 GMKKEFYSKAKLNADKWKKPGDIEEFYSKAKLNADK--WKKPG----DIEVKDVETHVAI 271
GM + Y +K D W + AD G DI V + ++ I
Sbjct: 1630 GMGMDLYKTSKAAQDVWNR--------------ADNHFKDTYGFSILDI-VINNPVNLTI 1674
Query: 272 HPGGDSD------------ESGDEEEKEEEKMDTE 294
H GG+ E+ + + + EK+ E
Sbjct: 1675 HFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE 1709
Score = 33.1 bits (75), Expect = 0.13
Identities = 46/228 (20%), Positives = 72/228 (31%), Gaps = 56/228 (24%)
Query: 1 MSHVGVYAEYQKANAGLVYDFQLINVEDFNGVGESEPNPYFY-QNLAEAEYCVALFMYMR 59
+ +GV +A +ED E P+P NL + + + Y+
Sbjct: 303 LFFIGVRC--YEAYP--NTSLPPSILEDSLENNEGVPSPMLSISNLTQEQ----VQDYVN 354
Query: 60 LL--GYPAHKITILSTYNGQKHLIRDVINTRCADNPLIGRPHKVTTVDKYQGQQNDYILL 117
PA K +S NG K+L+ + G P + Y L
Sbjct: 355 KTNSHLPAGKQVEISLVNGAKNLV------------VSGPPQSL------------YGLN 390
Query: 118 SLVRTASVGHLRDVRRLIVAMS-RARLGLYVFARVSL-FRNCFELTPAFNQLM------- 168
+R A D R + S R F V+ F + L PA + +
Sbjct: 391 LTLRKAKAPSGLDQSR--IPFSERKLKFSNRFLPVASPF-HSHLLVPASDLINKDLVKNN 447
Query: 169 --IRPQQLHIVP-HETFPTSRL---NTSRVPNSV--AIQDMVHMTTLV 208
+ + I P ++TF S L + S V I+ V T
Sbjct: 448 VSFNAKDIQI-PVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTT 494
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 39.0 bits (90), Expect = 0.001
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 99 HKVTTVDKYQGQQNDY-ILLSLVRTASVGHLRDVRRLIVAMSRARLGL 145
V TV + QG+ L+ L T RD ++V++SR L
Sbjct: 369 ADVHTVHEVQGETYADVSLVRLTPTPVSIIARDSPHVLVSLSRHTKSL 416
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.1 bits (72), Expect = 0.13
Identities = 9/77 (11%), Positives = 24/77 (31%), Gaps = 26/77 (33%)
Query: 220 KKEFYSKAKLNADKWKKPG--DIEEFYSKAKLNADKWKKPGDIEVKDVETHVAIHPGGDS 277
+ + SK +W++ D+EE+ + +K K
Sbjct: 100 ELDAASKVME--QEWREKAKKDLEEWNQRQSEQVEKNKI--------------------- 136
Query: 278 DESGDEEEKEEEKMDTE 294
+ ++ ++ D +
Sbjct: 137 -NNRIADKAFYQQPDAD 152
>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA;
1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X*
1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A*
3pwt_A* 3px7_A* 1ecl_A 1cy9_A* 1cyy_A*
Length = 592
Score = 32.2 bits (74), Expect = 0.21
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 7/33 (21%)
Query: 98 PHKVTTVDKYQGQQNDYILLSLVRTASVGHLRD 130
P K T++KY G +DY++ +SVGH+RD
Sbjct: 11 PAKAKTINKYLG--SDYVVK-----SSVGHIRD 36
>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga
maritima} PDB: 2gaj_A*
Length = 633
Score = 31.4 bits (72), Expect = 0.43
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 7/33 (21%)
Query: 98 PHKVTTVDKYQGQQNDYILLSLVRTASVGHLRD 130
P K T+ G N+Y + AS+GH+ D
Sbjct: 14 PAKAKTIKSILG--NEYEVF-----ASMGHIID 39
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1,
STR genomics, PSI-2, midwest center for structural
genomics; HET: MSE; 1.66A {Lactobacillus plantarum}
Length = 174
Score = 27.4 bits (61), Expect = 4.1
Identities = 9/58 (15%), Positives = 20/58 (34%)
Query: 91 DNPLIGRPHKVTTVDKYQGQQNDYILLSLVRTASVGHLRDVRRLIVAMSRARLGLYVF 148
+N + V +G + D +++ + + + L SRA L +
Sbjct: 94 ENQRLAPGVIVVPSFLAKGLEFDAVIVWNANQENYQREDERQLLYTICSRAMHELTLV 151
>1c17_M ATP synthase subunit A; membrane protein, helix, complex; NMR
{Escherichia coli} SCOP: f.18.1.1
Length = 177
Score = 26.5 bits (59), Expect = 7.8
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 8/69 (11%)
Query: 153 LFRNCFELTPAFNQLMIRPQQLHIVPHETFPTSRLNTSRVPNSVAIQDMVHMTTLVYNFY 212
N +L P I L + P++ +N V S+A+ ++ FY
Sbjct: 19 FLMNLMDLLPIDLLPYIAEHVLGLPALRVVPSADVN---VTLSMAL-----GVFILILFY 70
Query: 213 MDKVNGMKK 221
K+ G+
Sbjct: 71 SIKMKGIGG 79
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.135 0.399
Gapped
Lambda K H
0.267 0.0491 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,526,010
Number of extensions: 267564
Number of successful extensions: 503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 493
Number of HSP's successfully gapped: 22
Length of query: 294
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 201
Effective length of database: 4,105,140
Effective search space: 825133140
Effective search space used: 825133140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.3 bits)