RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4476
(266 letters)
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 109 bits (274), Expect = 3e-27
Identities = 60/145 (41%), Positives = 77/145 (53%), Gaps = 5/145 (3%)
Query: 13 HALDAGDELKLAATSYDASTPGSGPRSRGLRFRII-LPVTEVGLELKSSAGAPTESYHGL 71
+ GDE+ L + + RG R+ LELK S P
Sbjct: 243 LKVAIGDEMIL----WYSGMQHPDWEGRGYIVRLPNSFQDTFTLELKPSKTPPPTHLTTG 298
Query: 72 FCGPSFWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNL 131
F WK TS+DRMQ AL+KFA+D +S+S Y+Y+++LGH V ++ F LPK FS PN
Sbjct: 299 FTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNF 358
Query: 132 PDLNRSQVYAVKHAIQRPLSLIQGM 156
LN SQ AV H +QRPLSLIQG
Sbjct: 359 AQLNSSQSNAVSHVLQRPLSLIQGP 383
>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 = 107 bits (270), Expect = 8e-27
Identities = 73/144 (50%), Positives = 89/144 (61%), Gaps = 8/144 (5%)
Query: 15 LDAGDELKLAATSYDASTPGSGPRSRGLRFRIIL-PVTEVGLELKSSAGAPTESYHGLFC 73
L GDE+ L + G ++ E+ +EL+SS GAP E H
Sbjct: 66 LMQGDEICL----RYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHN--F 119
Query: 74 GPSF-WKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLP 132
F WKSTSFDRMQ AL+ FAVD+ SVS YIYH+LLGH V++V+ +C LPK F+A LP
Sbjct: 120 QVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLP 179
Query: 133 DLNRSQVYAVKHAIQRPLSLIQGM 156
DLN SQVYAVK +QRPLSLIQG
Sbjct: 180 DLNHSQVYAVKTVLQRPLSLIQGP 203
>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 = 105 bits (264), Expect = 5e-26
Identities = 67/106 (63%), Positives = 79/106 (74%), Gaps = 3/106 (2%)
Query: 52 EVGLELKSSAGAPTESYHGLFCGPSF-WKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLG 110
E+ +EL+SS GAP E H F WKSTSFDRMQ AL+ FAVD+ SVS YIYH+LLG
Sbjct: 276 EIAIELRSSVGAPVEVTHN--FQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLG 333
Query: 111 HNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGM 156
H V++V+ +C LPK F+A LPDLN SQVYAVK +QRPLSLIQG
Sbjct: 334 HEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGP 379
>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 = 37.3 bits (86), Expect = 0.004
Identities = 47/293 (16%), Positives = 76/293 (25%), Gaps = 121/293 (41%)
Query: 13 HALDAGDELKLAAT----SYDASTPGSGP--------------RSRGLR---FRIILP-V 50
L+ + L+ + Y S P S P + G R L
Sbjct: 211 QGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGA 270
Query: 51 TEVGLELKSS---AGAPTESYHGLFCGPSFWKSTSFDRMQLALRKFAVDDQSVSAYIYHR 107
T L ++ A + W+ SF A
Sbjct: 271 TGHSQGLVTAVAIAETDS------------WE--SF------------FVSVRKAI---- 300
Query: 108 LLGHNVDEVLF----RCHLPKHFSAPNLPDLNRSQVYAVKHAIQRP---LSLIQGMNQ-- 158
VLF RC+ + + +LP ++++ P LS I + Q
Sbjct: 301 -------TVLFFIGVRCY--EAYPNTSLPPSILED--SLENNEGVPSPMLS-ISNLTQEQ 348
Query: 159 ------RSNGLHHQPGGAGIG----NSAN--------------TNRLRNKSNLNHRPSGA 194
++N H P G + N A LR PSG
Sbjct: 349 VQDYVNKTN--SHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKA----KAPSGL 402
Query: 195 N----KLSQGHLSQGNNSQEITQPY-SQVMS----------QGGGFSLSQADL 232
+ S+ L N + P+ S ++ S + D+
Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDI 455
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Length = 608
Score = 33.2 bits (76), Expect = 0.090
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 83 FDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAV 142
+L L + ++++V+ + VDE L L K F + + Q A
Sbjct: 102 LCGDRLYLNRMWCNERTVARFFNEVNHAIEVDEALLAQTLDKLFPVSDEINW---QKVAA 158
Query: 143 KHAIQRPLSLIQG 155
A+ R +S+I G
Sbjct: 159 AVALTRRISVISG 171
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.3 bits (67), Expect = 0.42
Identities = 9/27 (33%), Positives = 9/27 (33%), Gaps = 9/27 (33%)
Query: 11 ELHALDAGDELKLAATSYDASTPGSGP 37
L L A LKL A S P
Sbjct: 21 ALKKLQA--SLKLYA-------DDSAP 38
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 29.4 bits (65), Expect = 1.3
Identities = 27/235 (11%), Positives = 59/235 (25%), Gaps = 84/235 (35%)
Query: 56 ELKSSA--GAP------TESYHGLFCGPSFWKSTSFDRMQLAL----------------R 91
+L P ES WK + D++ +
Sbjct: 317 DLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376
Query: 92 KFAV--DDQSVSAYIYHRL----LGHNVDEVLFRCH----LPKHFSAPNLPDLNRSQVYA 141
+ +V + + + + +V V+ + H + K + +
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ---------PKESTIS 427
Query: 142 VKHAIQRPLSLIQGMNQRSNGLHHQPGGAGIGNSANTNRLRNKSNLNHRPSGANKLSQGH 201
+ +I L ++ N+ + LH + + N+
Sbjct: 428 I-PSIYLEL-KVKLENEYA--LH--------------RSIVDHYNIP------KTFDSDD 463
Query: 202 LSQGNNSQEITQPYSQVMSQGGGFSLSQADLSQDSLMMSQLDGMLSQESAYLDHR 256
L Q YS + G L + + + + +LD R
Sbjct: 464 LIPPYLDQYF---YSHI-----GHHLKNIEHPERMTLFRMV---------FLDFR 501
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus
radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 27.0 bits (60), Expect = 8.7
Identities = 8/69 (11%), Positives = 20/69 (28%), Gaps = 3/69 (4%)
Query: 87 QLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAI 146
++ L ++ +++ I L D + L + Q +
Sbjct: 146 RIYLPHVLRAEKKLASLIRTLLATPPADGAGNDDWAVPKKARKGLSE---EQASVLDQLA 202
Query: 147 QRPLSLIQG 155
L ++ G
Sbjct: 203 GHRLVVLTG 211
>2hnh_A DNA polymerase III alpha subunit; DNA replication,
nucleotidyltransferase, beta, PHP, transferase; HET:
DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
Length = 910
Score = 26.7 bits (60), Expect = 9.4
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 9/27 (33%)
Query: 209 QEITQPYSQVM--SQG-GGFSLSQADL 232
QE QVM +Q G++L AD+
Sbjct: 687 QE------QVMQIAQVLSGYTLGGADM 707
>2ycd_A Glutathione S-transferase; SOIL bacteria, herbicide
detoxification; HET: GTB; 1.40A {Agrobacterium
tumefaciens} PDB: 3lq7_A
Length = 230
Score = 26.5 bits (59), Expect = 9.5
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 26 TSYDASTPGSGPRSRGLRFRIILPVTEVGLE 56
T ++ S G +R + R L EVG
Sbjct: 20 TVFERSPDGGRGLARDMPVRWAL--EEVGQP 48
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
0.315 0.131 0.386
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,816,908
Number of extensions: 210841
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 354
Number of HSP's successfully gapped: 11
Length of query: 266
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 174
Effective length of database: 4,133,061
Effective search space: 719152614
Effective search space used: 719152614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.5 bits)