RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16399
(165 letters)
>3a2k_A TRNA(Ile)-lysidine synthase; ligase, pseudo-knot, ligase/RNA
complex; 3.65A {Geobacillus kaustophilus}
Length = 464
Score = 51.6 bits (124), Expect = 1e-08
Identities = 11/49 (22%), Positives = 23/49 (46%)
Query: 112 EIHHTIVTNKLFEKHHRIAIAASGGKDSTVLAHVLKVLNEKYQYGLDLV 160
++ I ++L + + + SGG DS L HV L ++++ +
Sbjct: 4 KVRAFIHRHQLLSEGAAVIVGVSGGPDSLALLHVFLSLRDEWKLQVIAA 52
>1wy5_A TILS, hypothetical UPF0072 protein AQ_1887; N-type ATP-ppase,
structural genomics, translation, NPPSFA; 2.42A {Aquifex
aeolicus} SCOP: c.26.2.5 d.229.1.1 PDB: 2e21_A* 2e89_A*
Length = 317
Score = 51.1 bits (123), Expect = 2e-08
Identities = 15/51 (29%), Positives = 20/51 (39%)
Query: 104 CFFHAFELEIHHTIVTNKLFEKHHRIAIAASGGKDSTVLAHVLKVLNEKYQ 154
++ K+F R+ IA SGG DS VL VL L +
Sbjct: 2 NPESRVIRKVLALQNDEKIFSGERRVLIAFSGGVDSVVLTDVLLKLKNYFS 52
>1ni5_A Putative cell cycle protein MESJ; structural genomics, ATPase,
PP-type, putative cell cycle PR PSI, protein structure
initiative; 2.65A {Escherichia coli} SCOP: b.153.1.2
c.26.2.5 d.229.1.1
Length = 433
Score = 47.4 bits (113), Expect = 5e-07
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 116 TIVTNKLFEKHHRIAIAASGGKDSTVLAHVLKVLNEKYQYGLDLVLLSID 165
T+ N+ +I +A SGG DSTVL H L + G+ L + +
Sbjct: 3 TLTLNRQLLTSRQILVAFSGGLDSTVLLHQLVQWRTEN-PGVALRAIHVH 51
>3k32_A Uncharacterized protein MJ0690; predicted subunit of tRNA
methyltransferase, methanocaldococcus jannaschii DSM ,
PSI- 2; 2.50A {Methanocaldococcus jannaschii}
Length = 203
Score = 37.9 bits (88), Expect = 5e-04
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 128 RIAIAASGGKDSTVLAHVLKVLNEKYQYGLDLVLLSID 165
+ + SGGKDS++ A +LK + G + L++I+
Sbjct: 8 DVHVLFSGGKDSSLSAVILK------KLGYNPHLITIN 39
>1zun_A Sulfate adenylyltransferase subunit 2; beta barrel, switch domain,
heterodimer, pyrophosphate, G protein; HET: GDP AGS;
2.70A {Pseudomonas syringae} SCOP: c.26.2.2
Length = 325
Score = 33.6 bits (76), Expect = 0.019
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 107 HAFELEIHHTIVTNKLFEKHHRIAIAASGGKDSTVLAH-VLKVLNEKYQYGLDLVLLSID 165
H +LE + ++ + + S GKDS V+ H K + L ++ +D
Sbjct: 27 HLKQLEAESIHIIREVAAEFDNPVMLYSIGKDSAVMLHLARKAF---FPGKLPFPVMHVD 83
>2hma_A Probable tRNA (5-methylaminomethyl-2-thiouridylat
methyltransferase; alpha-beta, beta barrel, structural
genomics, PSI-2; HET: MSE SAM; 2.41A {Streptococcus
pneumoniae}
Length = 376
Score = 30.2 bits (69), Expect = 0.29
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 125 KHHRIAIAASGGKDSTVLAHVLK 147
R+ + SGG DS+V A +LK
Sbjct: 8 SKTRVVVGMSGGVDSSVTALLLK 30
>2der_A TRNA-specific 2-thiouridylase MNMA; protein-RNA complex,
transferase/RNA complex; 3.10A {Escherichia coli} PDB:
2det_A 2deu_A*
Length = 380
Score = 30.2 bits (69), Expect = 0.31
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 124 EKHHRIAIAASGGKDSTVLAHVLK 147
E ++ + SGG DS+V A +L+
Sbjct: 15 ETAKKVIVGMSGGVDSSVSAWLLQ 38
>1q15_A CARA; CMPR, (2S,5S)-5-carboxymethylproline, B-LS, B-lactam
synthetase, AS-B, class B asparagine synthetase,
AMP-CPP; 2.30A {Pectobacterium carotovorum} SCOP:
c.26.2.1 d.153.1.1 PDB: 1q19_A*
Length = 503
Score = 29.7 bits (67), Expect = 0.43
Identities = 22/140 (15%), Positives = 49/140 (35%), Gaps = 8/140 (5%)
Query: 21 KPLKYAYEKEIVMYAYYKKL--------VYFSTECIFAPNAYRGHARTFLKHLEKIRPAS 72
P+ K+ M K + ++F E + + R T +K+ ++++P +
Sbjct: 125 SPVHVVQGKKAWMTNSLKLVTAAEGEGALWFEEEALVCQSLMRADTYTPVKNAQRLKPGA 184
Query: 73 IMDIIHSESKYIEKNPANFNRPKTGDTLCKECFFHAFELEIHHTIVTNKLFEKHHRIAIA 132
+ + H Y P + L ++ + L + + I
Sbjct: 185 VHVLTHDSEGYSFVESRTLTTPASNQLLALPREPLLALIDRYLNAPLEDLAPRFDTVGIP 244
Query: 133 ASGGKDSTVLAHVLKVLNEK 152
SGG DS+++ + +K
Sbjct: 245 LSGGLDSSLVTALASRHFKK 264
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 29.2 bits (65), Expect = 0.54
Identities = 6/19 (31%), Positives = 7/19 (36%), Gaps = 1/19 (5%)
Query: 87 NPANF-NRPKTGDTLCKEC 104
P R GD +C C
Sbjct: 30 YPPKIVERFSEGDVVCALC 48
>1otk_A Protein PAAC, phenylacetic acid degradation protein PAAC;
structural genomics, PSI, protein structure initiative;
2.00A {Escherichia coli} SCOP: a.25.1.2 PDB: 3pvt_B*
3pvr_B* 3pvy_B* 3pw1_B* 3pw8_A* 3pwq_A
Length = 249
Score = 27.9 bits (62), Expect = 1.3
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 7/61 (11%)
Query: 56 GHARTFLKHLEKIRPASIMDII---HSESKYIEKNPANFNRPKT--GDTLCKECFFHAFE 110
G AR FL + ++ D + E ++ N +P DT+ ++ F A+
Sbjct: 48 GQARNFLSYAAELAGEGDEDTLAFTRDERQF--SNLLLVEQPNGNFADTIARQYFIDAWH 105
Query: 111 L 111
+
Sbjct: 106 V 106
>2oq2_A Phosphoadenosine phosphosulfate reductase; sulfate reduction, PAPS
reductase, oxidoreductase; HET: A3P; 2.10A
{Saccharomyces cerevisiae}
Length = 261
Score = 28.0 bits (62), Expect = 1.4
Identities = 3/24 (12%), Positives = 6/24 (25%)
Query: 123 FEKHHRIAIAASGGKDSTVLAHVL 146
+ + G V +L
Sbjct: 38 IVTFPHLFQTTAFGLTGLVTIDML 61
>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 = 27.5 bits (60), Expect = 2.4
Identities = 16/138 (11%), Positives = 34/138 (24%), Gaps = 49/138 (35%)
Query: 33 MYAYYKKLVYFSTECIFAPNAYRGHARTFLKHLEKIRPASIMDIIHSESKY--------- 83
+ +L +F P+A I P ++ +I +
Sbjct: 371 YRKMFDRLS------VFPPSA-------------HI-PTILLSLIWFDVIKSDVMVVVNK 410
Query: 84 ------IEKNPANFNRPKTGDTLCKECFFHAFELEIHHTIVTNKLFEKHHRIAIAASGGK 137
+EK P + LE+ + HR +
Sbjct: 411 LHKYSLVEKQPKEST-----------ISIPSIYLELKVKLENEY---ALHRSIVDHYNIP 456
Query: 138 DSTVLAHVLKVLNEKYQY 155
+ ++ ++Y Y
Sbjct: 457 KTFDSDDLIPPYLDQYFY 474
>2o8v_A Phosphoadenosine phosphosulfate reductase; disulfide crosslinked
complex, oxidoreductase; 3.00A {Escherichia coli}
Length = 252
Score = 27.0 bits (60), Expect = 3.0
Identities = 7/40 (17%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 126 HHRIAIAASGGKDSTVLAHVLKVLNEKYQYGLDLVLLSID 165
+++S G + V H++ Q D+ ++ D
Sbjct: 45 PGEYVLSSSFGIQAAVSLHLVN------QIRPDIPVILTD 78
>1sur_A PAPS reductase; assimilatory sulfate reduction,
3-phospho-adenylyl-sulfate reductase, oxidoreductase;
2.00A {Escherichia coli} SCOP: c.26.2.2
Length = 215
Score = 25.8 bits (57), Expect = 6.4
Identities = 7/40 (17%), Positives = 16/40 (40%), Gaps = 6/40 (15%)
Query: 126 HHRIAIAASGGKDSTVLAHVLKVLNEKYQYGLDLVLLSID 165
+++S G + V H++ Q D+ ++ D
Sbjct: 44 PGEYVLSSSFGIQAAVSLHLVN------QIRPDIPVILTD 77
>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 = 26.2 bits (57), Expect = 7.1
Identities = 11/77 (14%), Positives = 21/77 (27%), Gaps = 32/77 (41%)
Query: 39 KLVYFSTECIFAPNAYRGHA-RTFLKHLEK---------IRPASIMDIIHSES--KYIEK 86
++V+ YRG + + E I P + E+ +E+
Sbjct: 1784 EVVF-----------YRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVER 1832
Query: 87 N---------PANFNRP 94
N+N
Sbjct: 1833 VGKRTGWLVEIVNYNVE 1849
>2pg3_A Queuosine biosynthesis protein QUEC; YP_049261.1, hypothetical
protein, structural genomics, JOIN for structural
genomics; 2.40A {Pectobacterium atrosepticum SCRI1043}
SCOP: c.26.2.1
Length = 232
Score = 25.7 bits (57), Expect = 8.5
Identities = 9/32 (28%), Positives = 13/32 (40%), Gaps = 6/32 (18%)
Query: 134 SGGKDSTVLAHVLKVLNEKYQYGLDLVLLSID 165
SGG+DST Q D+ ++ D
Sbjct: 10 SGGQDSTTCLIQAL------QDYDDVHCITFD 35
>3bl5_A Queuosine biosynthesis protein QUEC; PREQ1 biosynthesis, RNA
modification, tRNA, hydrolase; 2.95A {Bacillus subtilis}
Length = 219
Score = 25.3 bits (56), Expect = 9.7
Identities = 6/32 (18%), Positives = 12/32 (37%), Gaps = 6/32 (18%)
Query: 134 SGGKDSTVLAHVLKVLNEKYQYGLDLVLLSID 165
SGG+DST + ++ ++
Sbjct: 11 SGGQDSTTCLLWAL------KEFEEVETVTFH 36
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
0.323 0.138 0.421
Gapped
Lambda K H
0.267 0.0530 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,598,342
Number of extensions: 142723
Number of successful extensions: 420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 420
Number of HSP's successfully gapped: 27
Length of query: 165
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 79
Effective length of database: 4,300,587
Effective search space: 339746373
Effective search space used: 339746373
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: 53 (24.7 bits)