RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16286
(92 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 = 48.7 bits (116), Expect = 2e-08
Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 6 NNVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSI 61
N H +GFL R+ VAL+RA+ G+ I+GN K LS LW + N ++ +
Sbjct: 554 ANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQ-PLWNHLLNYYKEQKVL 608
>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 = 48.0 bits (114), Expect = 4e-08
Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 7 NVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEI 51
N H +GFL R+ VAL+RA+ G+ I+GN K LS LW +
Sbjct: 731 NEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQ-PLWNHL 774
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 46.9 bits (111), Expect = 1e-07
Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 7 NVHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEI 51
N +GFL+ R+ V L+RAK GL I+GN + L+ + LW +
Sbjct: 733 NEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARN-TLWNHL 776
>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 = 33.0 bits (75), Expect = 0.008
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 20 RVC-VALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSINESFRLQCN 70
RV VAL+RAK+ LF++G+ K WQ ++ T + E R Q
Sbjct: 865 RVLYVALTRAKEKLFLIGSCKDHQKQLAKWQASASQ--TDWLLPEFDRYQAR 914
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 28.2 bits (62), Expect = 0.36
Identities = 9/59 (15%), Positives = 19/59 (32%), Gaps = 5/59 (8%)
Query: 8 VHNNVGFLKTVNRVCVALSRAKQGLFIMGNMKCLSADSQLWQEIKNKLVTRRSINESFR 66
+ V V+LSR + L + D L I++ + + ++
Sbjct: 392 PTPVSIIARDSPHVLVSLSRHTKSLKY----YTVVMDP-LVSIIRDLERVSSYLLDMYK 445
>4f3r_A Phosphopantetheine adenylyltransferase; phosphopantetheine
adenylyltranferase; 2.25A {Coxiella burnetii}
Length = 162
Score = 25.5 bits (57), Expect = 2.4
Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 20/74 (27%)
Query: 21 VCVALSRAKQGLFIMGNMKCLSAD---SQLWQEIKNKLVTRRSINE---SFRLQCNKHRA 74
V A + K + + + + ++ V + F H+A
Sbjct: 37 VACAPTSRKDPHL--------KLEERVNLIADVLTDERVEVLPLTGLLVDF---AKTHQA 85
Query: 75 VTII---RAVEDFE 85
I+ RAV DF+
Sbjct: 86 NFILRGLRAVSDFD 99
>3nv7_A Phosphopantetheine adenylyltransferase; helicobacter pylori 26695
strain, mutant I4V/N76Y, phosphopa adenylyltransferase;
1.75A {Helicobacter pylori} PDB: 3otw_A*
Length = 157
Score = 25.1 bits (56), Expect = 2.8
Identities = 5/20 (25%), Positives = 9/20 (45%), Gaps = 3/20 (15%)
Query: 69 CNKHRAVTII---RAVEDFE 85
++ ++ R V DFE
Sbjct: 78 AKEYHCKVLVRGLRVVSDFE 97
>3nd5_A Phosphopantetheine adenylyltransferase; PPAT, coenzyme A BIO
pathway; 2.30A {Enterococcus faecalis} PDB: 3nd6_A*
3nd7_A*
Length = 171
Score = 25.2 bits (56), Expect = 2.8
Identities = 15/82 (18%), Positives = 27/82 (32%), Gaps = 34/82 (41%)
Query: 21 VCVALSRAKQGLFIM--------------GNMKCLSADSQLWQEIKNKLVTRRSINESFR 66
+ V ++ +KQ LF N++ + ++QL V
Sbjct: 34 IGVFINTSKQTLFTPEEKKYLIEEATKEMPNVRVIMQETQL-------TVE-------S- 78
Query: 67 LQCNKHRAVTII---RAVEDFE 85
A +I R V+D+E
Sbjct: 79 --AKSLGANFLIRGIRNVKDYE 98
>3f3m_A Phosphopantetheine adenylyltransferase; PPAT, coenzyme A BIO
pathway, coenzyme A biosynthesis,
nucleotidyltransferase; HET: PPS; 2.40A {Staphylococcus
aureus}
Length = 168
Score = 24.4 bits (54), Expect = 5.9
Identities = 23/78 (29%), Positives = 29/78 (37%), Gaps = 27/78 (34%)
Query: 21 VCVALSRAKQGLFIMGNMKCLSAD------SQLWQEIKNKLVTRRSINESFR-LQ---CN 70
VCV + K+G F S + Q + + N V F L C
Sbjct: 35 VCVLKNSKKEGTF--------SLEERMDLIEQSVKHLPNVKV------HQFSGLLVDYCE 80
Query: 71 KHRAVTII---RAVEDFE 85
+ A TII RAV DFE
Sbjct: 81 QVGAKTIIRGLRAVSDFE 98
>3k9w_A Phosphopantetheine adenylyltransferase; niaid, ssgcid, seattle
structural genomics center for infect disease, coenzyme
A, COA; HET: 4PS ADE PG4; 1.60A {Burkholderia
pseudomallei} PDB: 3ikz_A* 3pxu_A*
Length = 187
Score = 24.5 bits (54), Expect = 6.4
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 3/20 (15%)
Query: 69 CNKHRAVTII---RAVEDFE 85
+ A I+ RAV DFE
Sbjct: 98 VRANDARVIVRGLRAVSDFE 117
>1o6b_A Phosphopantetheine adenylyltransferase; structural genomics; HET:
ADP; 2.20A {Bacillus subtilis} SCOP: c.26.1.3
Length = 169
Score = 24.0 bits (53), Expect = 7.9
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 3/20 (15%)
Query: 69 CNKHRAVTII---RAVEDFE 85
+ A I+ RAV DFE
Sbjct: 78 ARRKNAKAILRGLRAVSDFE 97
>1qjc_A Phosphopantetheine adenylyltransferase; coenzyme A biosynthesis,
nucleotidyltransferase; HET: PNS; 1.64A {Escherichia
coli} SCOP: c.26.1.3 PDB: 1h1t_A* 1gn8_A* 1b6t_A*
3l92_A* 3l93_A
Length = 158
Score = 24.0 bits (53), Expect = 7.9
Identities = 8/20 (40%), Positives = 9/20 (45%), Gaps = 3/20 (15%)
Query: 69 CNKHRAVTII---RAVEDFE 85
A +I RAV DFE
Sbjct: 77 ARNQHATVLIRGLRAVADFE 96
>3nbk_A Phosphopantetheine adenylyltransferase; PPAT, PHP; HET: PNS; 1.58A
{Mycobacterium tuberculosis} PDB: 3nba_A* 3pnb_A*
3lcj_A* 3rba_A* 1tfu_A* 3rff_A 3rhs_A*
Length = 177
Score = 24.0 bits (53), Expect = 8.4
Identities = 5/20 (25%), Positives = 6/20 (30%), Gaps = 3/20 (15%)
Query: 69 CNKHRAVTII---RAVEDFE 85
I+ R DFE
Sbjct: 97 VRSCGMTAIVKGLRTGTDFE 116
>1od6_A PPAT, phosphopantetheine adenylyltransferase; coenzyme A
biosynthesis, nucleotidyltransferase; HET: PNS; 1.5A
{Thermus thermophilus} SCOP: c.26.1.3
Length = 160
Score = 24.0 bits (53), Expect = 9.1
Identities = 7/20 (35%), Positives = 10/20 (50%), Gaps = 3/20 (15%)
Query: 69 CNKHRAVTII---RAVEDFE 85
+ A I+ RAV D+E
Sbjct: 78 VRRVGAQAIVKGLRAVSDYE 97
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
0.326 0.133 0.405
Gapped
Lambda K H
0.267 0.0834 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,259,142
Number of extensions: 56046
Number of successful extensions: 121
Number of sequences better than 10.0: 1
Number of HSP's gapped: 121
Number of HSP's successfully gapped: 15
Length of query: 92
Length of database: 6,701,793
Length adjustment: 59
Effective length of query: 33
Effective length of database: 5,054,454
Effective search space: 166796982
Effective search space used: 166796982
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.2 bits)