RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14016
(71 letters)
>3cuq_C Vacuolar protein-sorting-associated protein 25; ESCRT, MBV, VPS,
nucleus, protein transport, transc transcription
regulation, transport, endosome; 2.61A {Homo sapiens}
PDB: 2zme_C
Length = 176
Score = 87.7 bits (217), Expect = 4e-24
Identities = 32/67 (47%), Positives = 41/67 (61%)
Query: 2 SDVQWPWQYNFPPFFTLQPNEETRKKQLEAWRDLVLEYHKKTKTCIIDIQEADNTALFFN 61
+WPWQY FPPFFTLQPN +TR+KQL AW LVL + + K + + EA + LF N
Sbjct: 3 MSFEWPWQYRFPPFFTLQPNVDTRQKQLAAWCSLVLSFCRLHKQSSMTVMEAQESPLFNN 62
Query: 62 PAISSIL 68
+ L
Sbjct: 63 VKLQRKL 69
>1xb4_A VPS25, hypothetical 23.6 kDa protein in YUH1-URA8 intergenic
region; winged helix, unknown function; 3.10A
{Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 PDB:
1w7p_B 1u5t_C
Length = 202
Score = 75.9 bits (186), Expect = 3e-19
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 19/79 (24%)
Query: 5 QWPWQYNFPPFFTLQPNEETRKKQLEAWRDLVLEYHKKTKTCIIDI-------------- 50
P Y+FPP +T QPN TR++Q+ W D++ +Y K K + +
Sbjct: 3 ALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDSGS 62
Query: 51 -----QEADNTALFFNPAI 64
+ + LF N I
Sbjct: 63 TDNDDSKKISKNLFNNEDI 81
>1r8j_A KAIA; circadian clock protein; 2.03A {Synechococcus elongatus pcc
7942} SCOP: a.186.1.1 c.23.1.5 PDB: 1m2e_A 1m2f_A
Length = 289
Score = 27.3 bits (60), Expect = 0.41
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 15 FFTLQPNEETRK--KQLEA-WRDLVLEYHKKTKTCIIDIQEADNTALFFNPAISSILYAH 71
F P E++K + ++ +R++VL Y I N A F + ++ ++ H
Sbjct: 183 FLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIH 242
>1v2z_A Circadian clock protein KAIA homolog; all alpha, riken structural
genomics/proteomics initiative, structural genomics;
1.80A {Thermosynechococcus elongatus} SCOP: a.186.1.1
PDB: 1q6a_A 1q6b_A 1suy_A 1sv1_A
Length = 111
Score = 26.3 bits (58), Expect = 0.55
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 15 FFTLQPNEETRK--KQLEA-WRDLVLEYHKKTKTCIIDIQEADNTALFFNPAISSILYAH 71
FF + RK +L + +R +VLEY I E + A F + ++S +L H
Sbjct: 5 FFRRMSPADKRKLLDELRSIYRTIVLEYFNTDAKVNERIDEFVSKAFFADISVSQVLEIH 64
>1r5q_A KAI A, circadian oscillation regulator; four-helix-bundle, gene
regulation; 2.00A {Nostoc SP} SCOP: a.186.1.1
Length = 102
Score = 25.9 bits (57), Expect = 0.80
Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 4/54 (7%)
Query: 22 EETRKKQLEA----WRDLVLEYHKKTKTCIIDIQEADNTALFFNPAISSILYAH 71
E ++ L+ +R ++L Y K I + N N + I+ H
Sbjct: 4 EVDQQILLQQLKSDYRQILLSYFTTDKALKEKIDKFINAVFCANIPVPEIIEIH 57
>3mtu_A Tropomyosin alpha-1 chain, microtubule-associated RP/EB family
member 1; tropomysoin, overlap complex, coiled-coils,
contractIle PROT; HET: MSE; 2.10A {Gallus gallus} PDB:
3mud_C*
Length = 75
Score = 24.5 bits (53), Expect = 1.9
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 3/50 (6%)
Query: 21 NEETRKKQLEAWRDLVLEYHKKTKTCIIDIQEADNTALFFNPAISSILYA 70
N R +Q EA +D Y K + + QE + I ILYA
Sbjct: 20 NALDRAEQAEADKDF---YFGKLRNIELICQENEGENDPVLQRIVDILYA 66
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 25.1 bits (56), Expect = 2.1
Identities = 5/7 (71%), Positives = 6/7 (85%)
Query: 9 QYNFPPF 15
YNFPP+
Sbjct: 395 HYNFPPY 401
>2je6_B RRP41, exosome complex exonuclease 1; nuclease, hydrolase,
exonuclease, phosphorolytic, exoribonuclease, RNA
degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus}
SCOP: d.14.1.4 d.101.1.1 PDB: 2jea_B* 2jeb_B* 2br2_B
2c37_B* 2c38_B* 2c39_B* 3l7z_B
Length = 250
Score = 24.9 bits (55), Expect = 2.2
Identities = 3/7 (42%), Positives = 5/7 (71%)
Query: 9 QYNFPPF 15
+Y+ PF
Sbjct: 82 RYHMTPF 88
>3gme_A Polyribonucleotide nucleotidyltransferase; protein-RNA complex,
cytoplasm, nucleotidyltransferase, RNA- binding,
transferase, hydrolase; 2.40A {Escherichia coli E24377A}
PDB: 3gll_A 3gcm_A 3h1c_A 3cdj_A
Length = 549
Score = 25.2 bits (56), Expect = 2.2
Identities = 5/6 (83%), Positives = 6/6 (100%)
Query: 10 YNFPPF 15
YNFPP+
Sbjct: 380 YNFPPY 385
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 24.9 bits (55), Expect = 2.2
Identities = 5/7 (71%), Positives = 6/7 (85%)
Query: 9 QYNFPPF 15
YNFPP+
Sbjct: 420 NYNFPPY 426
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 25.1 bits (56), Expect = 2.3
Identities = 5/7 (71%), Positives = 6/7 (85%)
Query: 9 QYNFPPF 15
YNFPP+
Sbjct: 385 HYNFPPY 391
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 24.8 bits (55), Expect = 2.5
Identities = 4/6 (66%), Positives = 5/6 (83%)
Query: 10 YNFPPF 15
Y FPP+
Sbjct: 388 YEFPPY 393
>3bs0_A TODX; beta barrel, outer membrane protein, transport protein;
HET: C8E; 2.60A {Pseudomonas putida} PDB: 3brz_A*
Length = 439
Score = 24.4 bits (52), Expect = 4.2
Identities = 6/11 (54%), Positives = 6/11 (54%)
Query: 53 ADNTALFFNPA 63
N AL NPA
Sbjct: 25 TGNAALISNPA 35
>2r8u_A Microtubule-associated protein RP/EB family member 1; cytoskeleton,
acetylation, cell cycle, cell division, cytoplasm,
mitosis, phosphorylation; 1.35A {Homo sapiens} SCOP:
a.40.1.1 PDB: 1vka_A 1txq_B 1wu9_A 2hkq_A 2hl5_A 3tq7_A
3gjo_A 1yib_A 1yig_A
Length = 268
Score = 23.7 bits (50), Expect = 6.5
Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 23 ETRKKQLEAWRDLVLEYHKKTKTCIIDIQEADNTALFFNPAISSILYA 70
+ + LE RD Y K + + QE + I ILYA
Sbjct: 204 KLTVEDLEKERDF---YFGKLRNIELICQENEGENDPVLQRIVDILYA 248
>3lns_A Benzaldehyde dehydrogenase; oxidoreductase, NADP+, class 3
aldehyde dehyd adduct, covalent catalysis, mandelate
racemase pathway; HET: ZBZ NAP; 2.50A {Pseudomonas
putida} PDB: 3lv1_A*
Length = 457
Score = 23.9 bits (52), Expect = 6.6
Identities = 6/34 (17%), Positives = 13/34 (38%), Gaps = 7/34 (20%)
Query: 20 PNEETRKKQLEAWRDLVLEYHKKTKTCIIDIQEA 53
+ RK+ LE ++ V+ + + A
Sbjct: 47 ADVGFRKQSLERLKEAVINNKE-------ALYSA 73
>3h1t_A Type I site-specific restriction-modification system, R
(restriction) subunit; hydrolase, restriction enzyme
HSDR, ATP-binding; 2.30A {Vibrio vulnificus}
Length = 590
Score = 23.6 bits (51), Expect = 7.2
Identities = 8/44 (18%), Positives = 14/44 (31%), Gaps = 4/44 (9%)
Query: 21 NEETRKKQLEAWRDLVLEYHKKTKTCII---DIQEADNTALFFN 61
+ + D + + KT I+ D + AD N
Sbjct: 418 LKARTDAFAKHLTDFMKRTDRFAKT-IVFCVDQEHADEMRRALN 460
>3sza_A Aldehyde dehydrogenase, dimeric NADP-preferring; ALDH, rossmann
fold, oxidoreductase; 1.48A {Homo sapiens} PDB: 3szb_A*
1ad3_A*
Length = 469
Score = 23.3 bits (51), Expect = 9.5
Identities = 8/34 (23%), Positives = 15/34 (44%), Gaps = 7/34 (20%)
Query: 20 PNEETRKKQLEAWRDLVLEYHKKTKTCIIDIQEA 53
+ R +QLEA + L+ E + ++ A
Sbjct: 37 RPLQFRIQQLEALQRLIQEQEQ-------ELVGA 63
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
0.321 0.134 0.440
Gapped
Lambda K H
0.267 0.0837 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,062,523
Number of extensions: 45612
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 213
Number of HSP's successfully gapped: 19
Length of query: 71
Length of database: 6,701,793
Length adjustment: 41
Effective length of query: 30
Effective length of database: 5,557,032
Effective search space: 166710960
Effective search space used: 166710960
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 (21.9 bits)
S2: 51 (23.2 bits)