RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6931
(81 letters)
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease,
hydrolase, magnesium, metal nonsense-mediated mRNA
decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}
Length = 507
Score = 61.2 bits (147), Expect = 6e-13
Identities = 35/66 (53%), Positives = 50/66 (75%), Gaps = 4/66 (6%)
Query: 20 KAIKSALFVTIDGEFTGLNNGPN----TTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKY 75
+AI+ A F IDGEF+G+++GP+ T+ +DTP + Y K+++ SMDFLL QFGLCAFKY
Sbjct: 19 QAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKY 78
Query: 76 DNTTKR 81
D+T +
Sbjct: 79 DHTDSK 84
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain,
hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A
Length = 430
Score = 59.9 bits (144), Expect = 2e-12
Identities = 34/66 (51%), Positives = 47/66 (71%), Gaps = 4/66 (6%)
Query: 20 KAIKSALFVTIDGEFTGLNNGPN----TTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKY 75
+AI+ A F IDGEF+G+++GP+ T +DTP + Y K+++ SMDFLL QFGLC FKY
Sbjct: 17 QAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHSMDFLLFQFGLCTFKY 76
Query: 76 DNTTKR 81
D T +
Sbjct: 77 DYTDSK 82
>2d5r_A CCR4-NOT transcription complex subunit 7; poly(A) deadenylase,
antiproliferative protein, transcription; 2.50A {Homo
sapiens} SCOP: c.55.3.9
Length = 252
Score = 54.7 bits (131), Expect = 8e-11
Identities = 13/57 (22%), Positives = 20/57 (35%)
Query: 20 KAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76
+ I+ +V +D EF G+ P Y +R +IQ GL
Sbjct: 19 QVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQ 75
>1uoc_A POP2; hydrolase, DEDD nuclease, mRNA degradation, poly(A) tail,
transcription regulation, repressor, phosphorylation.;
2.3A {Saccharomyces cerevisiae} SCOP: c.55.3.9
Length = 289
Score = 53.9 bits (129), Expect = 2e-10
Identities = 13/57 (22%), Positives = 19/57 (33%)
Query: 20 KAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76
+ + V+I EF G P T +Y +R IQ GL +
Sbjct: 33 QLVSQYNHVSISTEFVGTLARPIGTFRSKVDYHYQTMRANVDFLNPIQLGLSLSDAN 89
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene
regulation; 1.40A {Schizosaccharomyces pombe} PDB:
3g0z_A 3g10_A
Length = 333
Score = 51.3 bits (122), Expect = 1e-09
Identities = 13/57 (22%), Positives = 22/57 (38%)
Query: 20 KAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76
I+ V++D EF G+ P + +Y +R +IQ GL +
Sbjct: 40 SLIERYPVVSMDTEFPGVVARPLGVFKSSDDYHYQTLRANVDSLKIIQIGLALSDEE 96
>3kzw_A Cytosol aminopeptidase; hydrolase, manganese binding, protease,
structural genomics; 2.70A {Staphylococcus aureus subsp}
Length = 515
Score = 25.8 bits (57), Expect = 1.7
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 3/24 (12%)
Query: 13 NITTRYAKAIKSALFVTIDGEFTG 36
N T KA+ +A FV F+G
Sbjct: 454 NHTNGQGKALFAASFV---THFSG 474
>2ztj_A Homocitrate synthase; (beta/alpha)8 TIM barrel, substrate complex,
amino-acid BIOS lysine biosynthesis, transferase; HET:
AKG; 1.80A {Thermus thermophilus} PDB: 2ztk_A* 2zyf_A*
3a9i_A*
Length = 382
Score = 25.6 bits (57), Expect = 1.7
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 39 NGPNTTPYDTPAQYYDKIRQ 58
+T TP Q Y +R+
Sbjct: 162 GLADTVGVATPRQVYALVRE 181
>3ivs_A Homocitrate synthase, mitochondrial; TIM barrel, metalloprotein,
transferase, claisen condensatio acid biosynthesis;
2.24A {Schizosaccharomyces pombe} PDB: 3ivt_A* 3ivu_A*
3mi3_A*
Length = 423
Score = 25.7 bits (57), Expect = 1.8
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 39 NGPNTTPYDTPAQYYDKIR 57
+T TP Q YD IR
Sbjct: 198 GIADTVGCATPRQVYDLIR 216
>1k0e_A P-aminobenzoate synthase component I; aminodeoxychorismate
synthase, chorismate, glutamine, tryptophan, PABA
synthase, lyase; HET: TRP; 2.00A {Escherichia coli}
SCOP: d.161.1.1 PDB: 1k0g_A*
Length = 453
Score = 25.2 bits (56), Expect = 2.7
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 47 DTPAQYYDKIRQGSMDFLL 65
D Y+ ++ LL
Sbjct: 16 DAAEFYFSRLSHLPWAMLL 34
>3rmj_A 2-isopropylmalate synthase; LEUA, truncation, neisseria MENI TIM
barrel, catalytic domain, dimer, leucine biosynthesis,
ketoisovalerate; 1.95A {Neisseria meningitidis}
Length = 370
Score = 24.8 bits (55), Expect = 3.3
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 39 NGPNTTPYDTPAQYYDKIRQ 58
N P+T Y P + + R+
Sbjct: 175 NIPDTVGYSIPYKTEEFFRE 194
>3ewb_X 2-isopropylmalate synthase; LEUA, structural genomics, unknown
function, amino-acid biosynthesis; 2.10A {Listeria
monocytogenes str}
Length = 293
Score = 24.8 bits (55), Expect = 3.9
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 39 NGPNTTPYDTPAQYYDKIRQ 58
N P+T Y P ++ +
Sbjct: 168 NIPDTVGYTNPTEFGQLFQD 187
>3eeg_A 2-isopropylmalate synthase; 11106D, beta barrel, PSI-II, structural
genomics, protein structure initiative; 2.78A {Cytophaga
hutchinsonii atcc 33406}
Length = 325
Score = 24.4 bits (54), Expect = 5.3
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 39 NGPNTTPYDTPAQYYDKIRQ 58
N P+TT Y P QY ++I+
Sbjct: 169 NIPDTTGYMLPWQYGERIKY 188
>3a1c_A Probable copper-exporting P-type ATPase A; ATP-binding, cell
membrane, copper transport, hydrolase, ION transport,
magnesium, membrane; HET: ACP; 1.85A {Archaeoglobus
fulgidus} PDB: 3a1d_A* 3a1e_A* 2b8e_A 2voy_J 2voy_I
Length = 287
Score = 24.4 bits (54), Expect = 5.7
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 16 TRYAKAIKSALFVTIDGEFTGL 37
+ + K+A+ V +G G+
Sbjct: 136 EKLEREAKTAVIVARNGRVEGI 157
>3ble_A Citramalate synthase from leptospira interrogans; TIM barrel,
licmsn, substrate specificity, acyltransferase,
amino-acid biosynthesis; 2.00A {Leptospira interrogans}
PDB: 3blf_A 3bli_A*
Length = 337
Score = 24.0 bits (53), Expect = 6.4
Identities = 3/20 (15%), Positives = 8/20 (40%)
Query: 39 NGPNTTPYDTPAQYYDKIRQ 58
P+T +P + + +
Sbjct: 187 FLPDTLGVLSPEETFQGVDS 206
>1ciy_A Cryia(A); toxin, ICP; 2.25A {Bacillus thuringiensis} SCOP: b.18.1.3
b.77.2.1 f.1.3.1
Length = 590
Score = 23.6 bits (50), Expect = 9.2
Identities = 9/44 (20%), Positives = 14/44 (31%)
Query: 11 QHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYD 54
++ + RYA +IDG N T + Q
Sbjct: 493 RYRVRIRYASTTNLQFHTSIDGRPINQGNFSATMSSGSNLQSGS 536
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
0.322 0.136 0.413
Gapped
Lambda K H
0.267 0.0819 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,191,645
Number of extensions: 56422
Number of successful extensions: 134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 132
Number of HSP's successfully gapped: 17
Length of query: 81
Length of database: 6,701,793
Length adjustment: 50
Effective length of query: 31
Effective length of database: 5,305,743
Effective search space: 164478033
Effective search space used: 164478033
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 (23.3 bits)