RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1354
(118 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 = 93.0 bits (231), Expect = 1e-23
Identities = 31/97 (31%), Positives = 55/97 (56%), Gaps = 10/97 (10%)
Query: 5 SGIPTDHIGVIATYRNQVSLLKRLLD----------KDIEINTVDQYQGRDKSIILYSST 54
+G D IG+I Y Q S L + + +++EI +VD +QGR+K I+ S
Sbjct: 493 AGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCV 552
Query: 55 CTSKSKESKILNDRKRLTVAISRAKHKLIILGDLQVI 91
++ + LND +RL VA++RA++ +II+G+ + +
Sbjct: 553 RANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKAL 589
>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 = 89.2 bits (221), Expect = 3e-22
Identities = 31/97 (31%), Positives = 55/97 (56%), Gaps = 10/97 (10%)
Query: 5 SGIPTDHIGVIATYRNQVSLLKRLLD----------KDIEINTVDQYQGRDKSIILYSST 54
+G D IG+I Y Q S L + + +++EI +VD +QGR+K I+ S
Sbjct: 669 AGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILSCV 728
Query: 55 CTSKSKESKILNDRKRLTVAISRAKHKLIILGDLQVI 91
++ + LND +RL VA++RA++ +II+G+ + +
Sbjct: 729 RANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKAL 765
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 87.7 bits (217), Expect = 1e-21
Identities = 28/97 (28%), Positives = 51/97 (52%), Gaps = 10/97 (10%)
Query: 5 SGIPTDHIGVIATYRNQVSLLKRLLD----------KDIEINTVDQYQGRDKSIILYSST 54
G+ + IGVI Y Q + + + + +E+ +VD +QGR+K I+ S
Sbjct: 671 DGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCV 730
Query: 55 CTSKSKESKILNDRKRLTVAISRAKHKLIILGDLQVI 91
++ + L D +RL V ++RAK+ L+ILG+ + +
Sbjct: 731 RANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSL 767
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 39.0 bits (90), Expect = 1e-04
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 1 MSLISGIPTDHIGVIATYRNQVSLLKRLLDKDIEINTVDQYQGRD-KSIILYSSTCTSKS 59
+ I+ + G I T+ Q L +++TV + QG + L T T
Sbjct: 338 AASINPVSKPLKGKILTFT-QSDKEALLSRGYADVHTVHEVQGETYADVSLVRLTPTP-- 394
Query: 60 KESKILNDRKRLTVAISRAKHKLI 83
S I D + V++SR L
Sbjct: 395 -VSIIARDSPHVLVSLSRHTKSLK 417
>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 = 35.5 bits (82), Expect = 0.002
Identities = 6/35 (17%), Positives = 11/35 (31%)
Query: 74 AISRAKHKLIILGDLQVIIAIVNCPNTGRYGNLGQ 108
A++RA+ + G R L +
Sbjct: 527 ALTRARDRFFSAGSASAWQIAAARQREARNTALLE 561
>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 = 34.6 bits (79), Expect = 0.004
Identities = 31/142 (21%), Positives = 42/142 (29%), Gaps = 47/142 (33%)
Query: 1 MSLISGIPTDHIGVIATYRNQVSLLKRL-LDKDIEI---NTVDQY--QGRDKSIILYS-- 52
M IS + + + N L K +EI N G +S LY
Sbjct: 338 MLSISNLTQEQVQDYVNKTNS-----HLPAGKQVEISLVNGAKNLVVSGPPQS--LYGLN 390
Query: 53 -----STCTSKSKESKI-LNDRK-----R-LTVAI-------SRAKHKLIILGDLQVI-- 91
+ S +S+I ++RK R L VA A I DL
Sbjct: 391 LTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDL--INKDLVKNNV 448
Query: 92 ------IAI-VNCPNTGRYGNL 106
I I V G +L
Sbjct: 449 SFNAKDIQIPVYDTFDGS--DL 468
>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 = 32.4 bits (74), Expect = 0.024
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 74 AISRAKHKLIILGDLQVIIAIVNCPNTGRYGNLGQ 108
A++RA+ +L + D +++ A + T R L
Sbjct: 569 AVTRARRRLSLYADERILSAAIATR-TERRSGLAA 602
>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 = 29.7 bits (67), Expect = 0.16
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 67 DRKRLTVAISRAKHKLIIL 85
+R+ L SRA H+L ++
Sbjct: 133 ERQLLYTICSRAMHELTLV 151
>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease,
double strand DNA repair, protein-DNA CO hydrolase-DNA
complex; HET: DNA; 2.80A {Bacillus subtilis} PDB:
3u44_A*
Length = 1232
Score = 28.0 bits (62), Expect = 0.83
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 73 VAISRAKHKLIILG 86
VA++RAK KL ++G
Sbjct: 869 VALTRAKEKLFLIG 882
>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 = 27.9 bits (61), Expect = 0.92
Identities = 14/121 (11%), Positives = 38/121 (31%), Gaps = 37/121 (30%)
Query: 1 MSLISGIPTDHIGVIATYRN-QVSLLKRLLDKDIEINTVDQYQGR---------DKSI-- 48
+S+I+ D + +++ L +++ + + +Y+ I
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389
Query: 49 ----ILYS-----------STCTSKS------KESKI-LND---RKRLTVAISRAKHKLI 83
+++ + S KES I + ++ + A H+ I
Sbjct: 390 ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI 449
Query: 84 I 84
+
Sbjct: 450 V 450
Score = 26.4 bits (57), Expect = 2.7
Identities = 6/37 (16%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 65 LNDRKRLTVAISRAKHKLIILGDLQ---VIIAI-VNC 97
+ R + ++ L++L ++Q A ++C
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC 266
>3lw5_N Photosystem I-N subunit, photosystem I reaction center subunit IX;
photosynthesis, electron transfer, membrane proteins,
large, complexes, chromophore; HET: CL1 PQN BCR LMU LMG;
3.30A {Pisum sativum} PDB: 2o01_N*
Length = 85
Score = 25.1 bits (54), Expect = 3.3
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 57 SKSKESKILNDRKRL-TVAISRAKHKLIILGDLQVIIAIVNCPNTGRYGNL 106
KSK +K LND+KRL T + A+ + G + C + + +
Sbjct: 8 EKSKTNKELNDKKRLATTGANFARAYTVEFGSCKFPENFTGCQDLAKQKKV 58
>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*
Length = 1180
Score = 26.1 bits (57), Expect = 3.7
Identities = 6/21 (28%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 65 LNDRKRLT-VAISRAKHKLII 84
L + RL VA++R+ +
Sbjct: 795 LAEDLRLLYVALTRSVWHCSL 815
>3dcn_A Cutinase, cutin hydrolase; catalytic triad, secreted, serine
esterase; 1.90A {Glomerella cingulata} PDB: 3dd5_A
3dea_A*
Length = 201
Score = 25.4 bits (55), Expect = 4.8
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 91 IIAIVNCPNTGRYGNLGQIPGTDGNRT 117
I +V T NLG+IP + ++T
Sbjct: 134 IKGVVLFGYTKNLQNLGRIPNFETSKT 160
>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit);
transcription factor, IKB/NFKB complex; 2.30A {Homo
sapiens} SCOP: d.211.1.1 PDB: 1nfi_E
Length = 236
Score = 24.4 bits (54), Expect = 9.7
Identities = 5/30 (16%), Positives = 15/30 (50%)
Query: 15 IATYRNQVSLLKRLLDKDIEINTVDQYQGR 44
+A+ + +++ L+ ++N + GR
Sbjct: 123 LASIHGYLGIVELLVSLGADVNAQEPCNGR 152
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
0.318 0.136 0.379
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: 1,714,501
Number of extensions: 88235
Number of successful extensions: 288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 282
Number of HSP's successfully gapped: 22
Length of query: 118
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 37
Effective length of database: 4,440,192
Effective search space: 164287104
Effective search space used: 164287104
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 (21.7 bits)
S2: 51 (24.0 bits)