RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16535
(333 letters)
>3a2k_A TRNA(Ile)-lysidine synthase; ligase, pseudo-knot, ligase/RNA
complex; 3.65A {Geobacillus kaustophilus}
Length = 464
Score = 55.8 bits (135), Expect = 6e-09
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 90 FRRQALDRGAAMLGVDCVATGHNADDIAETVLMNVLRG 127
R + VA GH+ DD ET+LM ++RG
Sbjct: 106 CRYRFFAELMEKHQAGYVAVGHHGDDQVETILMRLVRG 143
Score = 50.4 bits (121), Expect = 3e-07
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 24 FRRQALDRGAAMLGVDCVATGHNADDTDDIAETVLMNVLRG 64
R + VA GH+ DD ET+LM ++RG
Sbjct: 106 CRYRFFAELMEKHQAGYVAVGHHG---DDQVETILMRLVRG 143
>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 = 55.3 bits (134), Expect = 7e-09
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 90 FRRQALDRGAAMLGVDCVATGHNADDIAETVLMNVLRG 127
R + L G DC+AT H+ +D+ ET L+ RG
Sbjct: 112 LRYKFLKEILESEGFDCIATAHHLNDLLETSLLFFTRG 149
Score = 50.3 bits (121), Expect = 3e-07
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 24 FRRQALDRGAAMLGVDCVATGHNADDTDDIAETVLMNVLRG 64
R + L G DC+AT H+ +D ET L+ RG
Sbjct: 112 LRYKFLKEILESEGFDCIATAHHLNDL---LETSLLFFTRG 149
>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 = 50.9 bits (122), Expect = 3e-07
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 90 FRRQALDRGAAMLGVDCVATGHNADDIAETVLMNVLRG 127
R QA R +L + + T + DD ET L+ + RG
Sbjct: 97 ARYQAFAR--TLLPGEVLVTAQHLDDQCETFLLALKRG 132
Score = 45.5 bits (108), Expect = 1e-05
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 24 FRRQALDRGAAMLGVDCVATGHNADDTDDIAETVLMNVLRG 64
R QA R +L + + T + DD ET L+ + RG
Sbjct: 97 ARYQAFAR--TLLPGEVLVTAQHLDDQ---CETFLLALKRG 132
>3k32_A Uncharacterized protein MJ0690; predicted subunit of tRNA
methyltransferase, methanocaldococcus jannaschii DSM ,
PSI- 2; 2.50A {Methanocaldococcus jannaschii}
Length = 203
Score = 35.5 bits (82), Expect = 0.010
Identities = 18/139 (12%), Positives = 38/139 (27%), Gaps = 20/139 (14%)
Query: 75 IITIGRKNNCTFCGVFRRQALDRGAAMLGVDCVATGHNADDIAETVLMNVLRGDIARLQR 134
II + L+ A +A G DD + + ++ R
Sbjct: 77 IIEHKYPGPA--IQYVHKTVLEILAD--EYSILADGTRRDDRVPKLSYSEIQSLEMRKN- 131
Query: 135 CTDIITY-----AYEKEIV--MYAYYKKLVYFSTECIFAPNA-YRGHARTFLKHLEKIRP 186
I Y + + + + + + L + ++ Y R LK P
Sbjct: 132 ----IQYITPLMGFGYKTLRHLASEFFILEEIKSGTK--LSSDYEAEIRHILKERG-ESP 184
Query: 187 ASIMDIIHSGEQMAIKEGV 205
+ +K+ +
Sbjct: 185 EKYFPEHKQTRVVGLKKEI 203
Score = 30.5 bits (69), Expect = 0.45
Identities = 7/40 (17%), Positives = 11/40 (27%), Gaps = 4/40 (10%)
Query: 10 LEIGRKNNCTFCGVFRRQALDRGAAMLGVDCVATGHNADD 49
+E + L+ A +A G DD
Sbjct: 78 IEHKYPGPA--IQYVHKTVLEILAD--EYSILADGTRRDD 113
>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 = 36.8 bits (84), Expect = 0.010
Identities = 30/303 (9%), Positives = 78/303 (25%), Gaps = 100/303 (33%)
Query: 114 DDIAETVLMNVLRGDIARLQRC-----------TDIITYAYEKEIVMYAYYKKLVYFSTE 162
++ N ++ C TD ++ A I + + L +
Sbjct: 251 LNVQNAKAWNAF--NL----SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK 304
Query: 163 CIFA-----------PNAYRGH---------------AR-TFLKH-----LEKIRPASIM 190
+ + A KH L I +S+
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL- 363
Query: 191 DIIHSGE------QMAI-KEGVKLPNREVCELCGFLSSQKI------CKACSLLEGLNK- 236
+++ E ++++ +P + + + + SL+E K
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423
Query: 237 ---GLPKLSLSKRSVQDRIRQ------ENYSKVQSITGYRDDSLETVKQNKEDY------ 281
+P + L + + ++Y+ + + D L + + Y
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPK---TFDSDDL--IPPYLDQYFYSHIG 478
Query: 282 ------QMDLKILSYDELY---GWTMDAIVNQGIGPRSPACKERSDHYAMGADMKSFK-- 330
+ ++ + ++ + I + A +K +K
Sbjct: 479 HHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDS-----TAWNASGSILNTLQQLKFYKPY 533
Query: 331 IQE 333
I +
Sbjct: 534 ICD 536
Score = 36.4 bits (83), Expect = 0.015
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 10/95 (10%)
Query: 238 LPKLSLSKRSVQDRIRQENYSKVQSITGYR-DDSLETVKQNKEDYQMDLK-ILSYDELYG 295
+PK LSK + D I + + R +L + + +E Q ++ +L + Y
Sbjct: 41 MPKSILSKEEI-DHIIMSKDAVSGT---LRLFWTLLS--KQEEMVQKFVEEVLRIN--YK 92
Query: 296 WTMDAIVNQGIGPRSPACKERSDHYAMGADMKSFK 330
+ M I + P + D + F
Sbjct: 93 FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA 127
>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 = 36.6 bits (84), Expect = 0.011
Identities = 29/152 (19%), Positives = 46/152 (30%), Gaps = 47/152 (30%)
Query: 39 DCVATGH----------NAD--DTDDIAETVLMNVLRGDIARLQRCTDIITIGRKNNCTF 86
A GH AD + + E V RG +Q +GR N
Sbjct: 1757 ATFA-GHSLGEYAALASLADVMSIESLVEVV---FYRGMT--MQVAVPRDELGRSN---- 1806
Query: 87 CGVFRRQALDRGAAMLGVD-------CVATGHNADDIAETVLMN--------VLRGDIAR 131
G+ A++ G G + E V N V GD+
Sbjct: 1807 YGMI---AINPGRVAASFSQEALQYVVERVGKRTGWLVEIV--NYNVENQQYVAAGDLRA 1861
Query: 132 LQRCTDIITYAYEKEIVMYAYYKKL-VYFSTE 162
L T+++ + ++I + +L S E
Sbjct: 1862 LDTVTNVLNFIKLQKIDI----IELQKSLSLE 1889
Score = 34.6 bits (79), Expect = 0.054
Identities = 18/110 (16%), Positives = 34/110 (30%), Gaps = 30/110 (27%)
Query: 23 VFRR-----QALDRGA------AMLGVD--CVATGHNADDTDDIAETVLM---------N 60
VF R A+ R M+ ++ VA + + + E V N
Sbjct: 1786 VFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVN 1845
Query: 61 --------VLRGDIARLQRCTDIITIGRKNNCTFCGVFRRQALDRGAAML 102
V GD+ L T+++ + + + +L+ L
Sbjct: 1846 YNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEGHL 1895
Score = 33.1 bits (75), Expect = 0.16
Identities = 36/320 (11%), Positives = 74/320 (23%), Gaps = 118/320 (36%)
Query: 1 VQLTHWTLDLEIGRKNNCTFCGVFRRQALDRGAAMLGVDCVATGHNADDTDDIAETVLMN 60
+QL H+ + ++ + A ++ +A + + +
Sbjct: 244 IQLAHYVVTAKLLGFTPGELRSYLK-GATGHSQGLVTAVAIAETDSWESFFVSVRKAITV 302
Query: 61 VLR-GDIARLQRCTDIITIGRKNNCTFCGVFRRQALDRGAAMLGVDCVATGHNADDIAET 119
+ G R + +L ++L D + +
Sbjct: 303 LFFIG--VRCYEA-----------------YPNTSLP--PSILE-DSLENNEGV----PS 336
Query: 120 VLMNVLRG-DIARLQRCTDIITYAYEKEIVMYAYYKKLVYFSTECIFAPNAYRGHARTFL 178
M + ++Q +
Sbjct: 337 -PMLSISNLTQEQVQD--------------------------------------YVNKTN 357
Query: 179 KHLEKIRPASIMDIIHSGEQMAIKEGVKLPNREVCELCGFLSSQKICKACSLLEGLNKGL 238
HL + I ++ G V + G S L GLN L
Sbjct: 358 SHLPAGKQVEI----------SLVNG---AKNLV--VSGPPQS---------LYGLNLTL 393
Query: 239 PKLSLSKRSVQDRIRQENYSKVQSITGYR-------------DDSLETVKQNKEDYQM-- 283
K Q RI +S+ + R + + + ++ +
Sbjct: 394 RKAKAPSGLDQSRIP---FSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSF 450
Query: 284 ---DLKILSYDELYGWTMDA 300
D++I YD T D
Sbjct: 451 NAKDIQIPVYD-----TFDG 465
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 27.9 bits (63), Expect = 6.0
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 108 ATGHNADDIAETVLMNVLRGDIARLQRCTDII 139
AT HNA +I VL GD +++ D+I
Sbjct: 366 ATLHNASEIKR---KGVLIGDTVVIRKAGDVI 394
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 27.5 bits (62), Expect = 6.7
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 108 ATGHNADDIAETVLMNVLRGDIARLQRCTDII 139
T HN I E +++ GD + + +I
Sbjct: 354 VTLHNESYIEE---LDIRIGDWVLVHKAGGVI 382
>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 = 27.5 bits (62), Expect = 6.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 29 LDRGAAMLGVDCVATGH 45
L+ A LG D +ATGH
Sbjct: 124 LEFAAEDLGADYIATGH 140
Score = 27.5 bits (62), Expect = 6.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 95 LDRGAAMLGVDCVATGH 111
L+ A LG D +ATGH
Sbjct: 124 LEFAAEDLGADYIATGH 140
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 27.5 bits (62), Expect = 8.4
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 108 ATGHNADDIAETVLMNVLRGDIARLQRCTDII 139
AT HNAD+I + + GD ++R D+I
Sbjct: 356 ATLHNADEIER---LGLRIGDKVVIRRAGDVI 384
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 0.137 0.411
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,107,535
Number of extensions: 305811
Number of successful extensions: 648
Number of sequences better than 10.0: 1
Number of HSP's gapped: 641
Number of HSP's successfully gapped: 25
Length of query: 333
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 239
Effective length of database: 4,077,219
Effective search space: 974455341
Effective search space used: 974455341
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: 57 (25.6 bits)