RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2094
(341 letters)
>2exn_A Hypothetical protein BOR11; beta barrel containing fold,
autostructure, autoassign, structure, structural
genomics, PSI; NMR {Bordetella bronchiseptica} SCOP:
b.165.1.1
Length = 136
Score = 66.8 bits (163), Expect = 7e-14
Identities = 24/160 (15%), Positives = 49/160 (30%), Gaps = 25/160 (15%)
Query: 25 VTEINIYPLKSGYYLSVEKAFCDFKGLSRIGQGYPLSDRCFLLFNRSKGTYISNIAHNRL 84
++ P+ + +A + +L+ N G +++ RL
Sbjct: 1 MSTTAYQPIAECGATTQSEAA--------------AYQKRWLVAN-DAGQWLNRDLCPRL 45
Query: 85 VLVKVTALDKDLIQFSVHNDDTYT-PFVLNMADFNRSGSVHTIRMYEKDLVHAFDCGDAA 143
V V L + P + D + + + E+ V D G+ A
Sbjct: 46 AEVSVE-LRMGYLVLKAPGMLRLDIPLDVIEDDDSVRYQM---LVGEQT-VDVVDEGELA 100
Query: 144 SEWFSRFLLGKEDPDIRLGYDCDEQRKLNGTIYERYRHHY 183
+ W S G R+ + ++ E + HH+
Sbjct: 101 AAWISNH-AGV---PCRILKVHPDMAEVRWPSLEHHHHHH 136
>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 = 47.5 bits (112), Expect = 4e-06
Identities = 41/325 (12%), Positives = 99/325 (30%), Gaps = 99/325 (30%)
Query: 46 CDFKGLSR-IGQGYPL-------SDRCFL-LFNRSKGTYISNIAHNRLVLVKVTALDKDL 96
C + L R + P S R L ++ K +++ ++ + L+
Sbjct: 313 CRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK--HVNCDKLTTIIESSLNVLEPAE 370
Query: 97 IQ-----FSVHNDDTYTPFVLNMADFNRSGSVHTIRMYEKDLVHAFDCGDAASEWFSRFL 151
+ SV + P + + D++ D ++ L
Sbjct: 371 YRKMFDRLSVFPPSAHIP-------------TILLSLIWFDVIK-SDVMVVVNKLHKYSL 416
Query: 152 LGKEDPDIRLG-YD--------CDEQRKLNGTIYERY---RHHYGDHIT--NEDMGKYAY 197
+ K+ + + + + L+ +I + Y + D + D Y++
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476
Query: 198 LASYMLMNEASVKDLNERLQLKGETEVSIHNFRGNIILSTDQAYEEDNWDWVRLNEDIIL 257
+ + L N + ER+ L FR + L ++ ++ + I
Sbjct: 477 IG-HHLKN----IEHPERMTL----------FR-MVFL---------DFRFLE--QKIRH 509
Query: 258 RGMKPCTRCTMTCLDPETGQKNLRTEPLKTLRSYRGPIGEK-------ARALEKGSPRLG 310
++ N L+ L+ Y+ I + A+ P++
Sbjct: 510 DSTAWNASGSIL---------NT----LQQLKFYKPYICDNDPKYERLVNAILDFLPKIE 556
Query: 311 --LYCGLYSRGTVQ-----KGDPVY 328
L C Y+ ++ + + ++
Sbjct: 557 ENLICSKYTD-LLRIALMAEDEAIF 580
Score = 40.6 bits (94), Expect = 7e-04
Identities = 28/190 (14%), Positives = 62/190 (32%), Gaps = 27/190 (14%)
Query: 116 DFNRSGSVHT----IRMYEKDLVHAFDCGDAASEWFSRFLLGKEDPDIRLGYDCDEQR-- 169
DF + + ++E V FDC D + + +L KE+ D +
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDV--QDMPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 170 KLNGTIYERYRHHYGDHITNEDMGKYAYLASYM-------LMNEASVKDLNERLQLKGET 222
+L T+ + + Y +L S + M + +RL +
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 223 EVSIHNFRGNIILSTDQAYEEDNWDWVRLNEDIILRGMKPCTRCTMTCLDPETGQKNLRT 282
+ R L QA E +R +++++ G+ + T + + +
Sbjct: 126 FAKYNVSRLQPYLKLRQALLE-----LRPAKNVLIDGVLGSGK---TWVALDV----CLS 173
Query: 283 EPLKTLRSYR 292
++ ++
Sbjct: 174 YKVQCKMDFK 183
Score = 35.6 bits (81), Expect = 0.025
Identities = 23/126 (18%), Positives = 37/126 (29%), Gaps = 24/126 (19%)
Query: 28 INIYPLKSGYY------LSVEKAFCDFKG--LSRIGQG--YPLSDRCFLLFN--RSKGTY 75
++ Y + + +++ F G L I L FL F K
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQK--- 506
Query: 76 ISNIAHNRLVLVKVTALDKDLIQFSVH------NDDTYTPFVLNMADFNRSGSVHTIRMY 129
I H+ ++ L Q + ND Y V + DF + I
Sbjct: 507 ---IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSK 563
Query: 130 EKDLVH 135
DL+
Sbjct: 564 YTDLLR 569
Score = 29.4 bits (65), Expect = 2.2
Identities = 26/175 (14%), Positives = 52/175 (29%), Gaps = 53/175 (30%)
Query: 179 YRHHYGDHITNEDMGKYAYLASYMLMNEASVKDLN-----------------ERLQLKGE 221
+ HH+ D T E +Y + S +A V + + + + + +
Sbjct: 2 HHHHHMDFETGEHQYQYKDILSVFE--DAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKD 59
Query: 222 TEVSIHNFRGNIILSTDQAYE-------EDNWDWVRLNEDIILRGMKPC--TRCTMTCLD 272
++ ++ + N+ + L I +P TR + D
Sbjct: 60 AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF--LMSPIKTEQRQPSMMTRMYIEQRD 117
Query: 273 P--ETGQK----NL-RTEPLKTLRSYRGPIGEKARALEKGSP--RLGLY----CG 314
Q N+ R +P LR +AL + P + + G
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLR----------QALLELRPAKNVLIDGVLGSG 162
>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 = 40.0 bits (93), Expect = 0.001
Identities = 46/262 (17%), Positives = 80/262 (30%), Gaps = 106/262 (40%)
Query: 49 KGLSRI-----GQGYPLSDRCF--L--LFNRSKGTYISNI------AHNRLV-LVKV--- 89
+G +++ GQG +D F L L+ TY + + L L++
Sbjct: 151 EGNAQLVAIFGGQGN--TDDYFEELRDLYQ----TYHVLVGDLIKFSAETLSELIRTTLD 204
Query: 90 -------------------TALDKD-------------LIQFS----VHNDDTYTPFVLN 113
DKD +IQ + +TP
Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPG--E 262
Query: 114 MADFNRSGSVHTIRMYEKDLVHAFDCGDAASEW--FSR---------FLLGKEDPDIRLG 162
+ + + + H+ + LV A W F F +G +R
Sbjct: 263 LRSYLKGATGHS-----QGLVTAVAIA-ETDSWESFFVSVRKAITVLFFIG-----VR-C 310
Query: 163 YDCDEQRKLNGTIYERYRHHYGDHITNEDMGKYAYLASYML----MN----EASVKDLNE 214
Y+ L +I E D + N + G + S ML + + V N
Sbjct: 311 YEAYPNTSLPPSILE-------DSLENNE-G----VPSPMLSISNLTQEQVQDYVNKTNS 358
Query: 215 RLQLKGETEVSIHNFRGNIILS 236
L + E+S+ N N+++S
Sbjct: 359 HLPAGKQVEISLVNGAKNLVVS 380
Score = 33.5 bits (76), Expect = 0.11
Identities = 69/395 (17%), Positives = 107/395 (27%), Gaps = 178/395 (45%)
Query: 23 GYVTEINIYPLKSGYYLSV-EKAFCDFKGLSRIGQGYPLSDRCFLLFNRSKGTYISNIAH 81
GYV+ + P K G + V +F + C+L N +I H
Sbjct: 66 GYVSS-LVEPSKVGQFDQVLNLCLTEF-------------ENCYLEGN--------DI-H 102
Query: 82 N---RLVLVKVTALDK--DLIQFSVHNDDTYTP--FVLNMADFNRSGSVHTIRMYEKDLV 134
+L+ T L K +LI+ Y + +S S L
Sbjct: 103 ALAAKLLQENDTTLVKTKELIK-------NYITARIMAKRPFDKKSNS---------ALF 146
Query: 135 HAFDCGDA-----------ASEWFSRFLLGKEDPDIRLGYDCDEQRKLNGTIYERYRHHY 183
A G+A ++F +E R L Y+ Y
Sbjct: 147 RAVGEGNAQLVAIFGGQGNTDDYF------------------EELRDL----YQTYHVLV 184
Query: 184 GDHI------------TNEDMGKY--------------------AYLAS----------- 200
GD I T D K YL S
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVI 244
Query: 201 ----YMLMNEA---SVKDLNERLQLKGETEVSIHNFRGNIILSTDQAYEEDNWD-WVRLN 252
Y++ + + +L L+ G T S ++ + A E D+W+ +
Sbjct: 245 QLAHYVVTAKLLGFTPGELRSYLK--GATGHS-----QGLVTAVAIA-ETDSWESFFVSV 296
Query: 253 EDII-------LRGMKPCTRCT-MTCLDPETGQKNLRTEPLKTLRSYRGPIGEKARALEK 304
I +R C T L P + +L E
Sbjct: 297 RKAITVLFFIGVR----CYEAYPNTSLPPSILEDSLEN-------------NEGVP---- 335
Query: 305 GSPRLGLYCGLYSRGTVQKGDPVYVAVSEKLNAKV 339
SP L + L ++ VQ YV K N+ +
Sbjct: 336 -SPMLSI-SNL-TQEQVQD----YV---NKTNSHL 360
>2k3j_A Mitochondrial intermembrane space import and assembly protein 40;
alpha-hairpin fold, coiled coil-helix-coiled coil-helix
domain; NMR {Homo sapiens} PDB: 2l0y_A
Length = 146
Score = 30.6 bits (68), Expect = 0.35
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 3/53 (5%)
Query: 139 CGDAASEWFSRFLLGKEDPDIRLGYDCDEQRKLNGTIYERYRHHYGDHITNED 191
CG+ FS F E+ G DC +Q + ++Y Y +E+
Sbjct: 68 CGEQFKSAFSCFHYSTEEIK---GSDCVDQFRAMQECMQKYPDLYPQEDEDEE 117
>2zxt_A Maltose-binding periplasmic protein, linker, MITO intermembrane
space import AND...; disulfide bond, alpha helix,
fusion, sugar transport; HET: MAL; 3.00A {Escherichia
coli}
Length = 465
Score = 31.4 bits (71), Expect = 0.45
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 139 CGDAASEWFSRFLLGKEDPDIRLGYDCDEQRKLNGTIYERYRHHYGDHITNED 191
CG+ FS F+ + +P G DC E+ + + +Y HY + +
Sbjct: 407 CGEEFKSAFSCFVYSEAEPK---GIDCVEKFQHMQDCFRKYPEHYAEQLKETS 456
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA
replication, DNA-BI DNA-directed DNA polymerase,
exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A
{Saccharomyces cerevisiae}
Length = 919
Score = 30.3 bits (68), Expect = 1.2
Identities = 13/94 (13%), Positives = 31/94 (32%), Gaps = 17/94 (18%)
Query: 97 IQFSVHNDDTYTPFVLNMADFNRSGSVHTIRMY----EKDLVHAFDCGDAASEWFSRFLL 152
I V PF+ N+ N + ++ E++++ + + +
Sbjct: 276 IANVVSIAGAKKPFIRNVFTLNTCSPITGSMIFSHATEEEMLSNW------RNFIIKV-- 327
Query: 153 GKEDPDIRLGYDCDEQRKLNGTIYERYRHHYGDH 186
DPD+ +GY+ + R + +
Sbjct: 328 ---DPDVIIGYNT--TNFDIPYLLNRAKALKVND 356
>3mve_A FRSA, UPF0255 protein VV1_0328; FRSA,fermentation/respiration
switch protein, hydrolase ACTI lyase; 2.20A {Vibrio
vulnificus} PDB: 3our_A
Length = 415
Score = 30.0 bits (67), Expect = 1.4
Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 1/50 (2%)
Query: 104 DDTYTPFVLNMADFNRSGSVHTIRMYEKDLVHAFDC-GDAASEWFSRFLL 152
D +P+ N S ++ K + ++ D A +W LL
Sbjct: 365 GDPVSPYSDNQMVAFFSTYGKAKKISSKTITQGYEQSLDLAIKWLEDELL 414
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.4 bits (62), Expect = 2.1
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 18/45 (40%)
Query: 297 EKARALEKGSPRLGLYCGLYSRGTVQKGD--PVYVAVSEKLNAKV 339
EK +AL+K L LY D P A++ + A +
Sbjct: 18 EK-QALKKLQASLKLY----------ADDSAP---ALA--IKATM 46
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA
repair, DNA-binding; HET: DNA DOC DCP; 1.92A
{Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A*
3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
Length = 786
Score = 28.9 bits (65), Expect = 2.9
Identities = 11/79 (13%), Positives = 26/79 (32%), Gaps = 13/79 (16%)
Query: 90 TALDKDLIQFSVHNDDTYTPFVLNMADFNRSGSVHTIRMY--EKDLVHAFDCGDAASEWF 147
T +L + ++L + + S + L+ + WF
Sbjct: 162 TTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVASRPQLLEKL------NAWF 215
Query: 148 SRFLLGKEDPDIRLGYDCD 166
+ + DPD+ +G++
Sbjct: 216 ANY-----DPDVIIGWNVV 229
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 28.2 bits (64), Expect = 5.2
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 161 LGYDCDEQR--KLNGTIYERYRHHY 183
LG D Q +L G + + HY
Sbjct: 362 LGTARDAQVLDELMGERTDTFLFHY 386
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 27.8 bits (63), Expect = 6.0
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 161 LGYDCDEQR--KLNGTIYERYRHHY 183
LG DEQ L GT E + HY
Sbjct: 372 LGTGDDEQFIDALEGTYKESFLLHY 396
>3o0q_A Ribonucleoside-diphosphate reductase; alpha/beta barrel,
adenosylcobalamin dependent, ribonucle reductase; HET:
TTP GDP ADN; 1.80A {Thermotoga maritima} PDB: 1xjf_A*
1xjg_A* 1xje_A* 1xjk_A* 1xjm_A* 1xjn_A* 3o0n_A* 3o0o_A*
1xjj_A*
Length = 644
Score = 27.7 bits (62), Expect = 6.0
Identities = 14/106 (13%), Positives = 22/106 (20%), Gaps = 34/106 (32%)
Query: 160 RLGYDCDEQRKLNGTIYERYRHHYGDHITNEDMGKYAYLASYMLMNEASVKDLNERLQLK 219
+ Y+ E R + H A+ SY L E K
Sbjct: 404 EIPYNSQEARDFAANLMAFIALH-------------AHRTSYELGKE------------K 438
Query: 220 GETEVSIHNFRGNIILSTDQAYEEDN-----WDWVRLNEDIILRGM 260
G + + D D +R +
Sbjct: 439 GNFP----LLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFR 480
>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 = 27.5 bits (62), Expect = 7.3
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 161 LGYDCDEQR--KLNGTIYERYRHHY 183
LG D Q +L G + + HY
Sbjct: 356 LGTARDAQVLDELMGERTDTFLFHY 380
>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 = 27.6 bits (62), Expect = 7.4
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 161 LGYDCDEQR--KLNGTIYERYRHHY 183
L EQ+ L+ +RY H+Y
Sbjct: 397 LNMLRMEQQLDTLSPVTRKRYMHNY 421
>1jms_A Terminal deoxynucleotidyltransferase; polymerase; 2.36A {Mus
musculus} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB:
1kdh_A* 1kej_A*
Length = 381
Score = 27.2 bits (59), Expect = 8.8
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 184 GDHITNEDMGKYAYLASYMLMNEASVKDLNERLQLKGETEVSIHNFRG 231
G D+ +YA M+++ ++ D +R+ L+ E+E I G
Sbjct: 323 GSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLG 370
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
e.8.1.1
Length = 847
Score = 27.1 bits (60), Expect = 9.4
Identities = 15/72 (20%), Positives = 23/72 (31%), Gaps = 9/72 (12%)
Query: 96 LIQFSVHNDD-TYTPFVLNMADFNRSGSVHTIRMYEKDLVHAFDCGDAASEWFSRFLLGK 154
+I ++ D VLN D N + V F+ F LL
Sbjct: 217 IISIALAGSDGLKKVLVLNRNDVNEGSV-----KLDGISVERFNTEYELLGRFFDILL-- 269
Query: 155 EDPDIRLGYDCD 166
+ I L ++ D
Sbjct: 270 -EYPIVLTFNGD 280
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
0.320 0.138 0.420
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: 5,332,634
Number of extensions: 316452
Number of successful extensions: 570
Number of sequences better than 10.0: 1
Number of HSP's gapped: 560
Number of HSP's successfully gapped: 23
Length of query: 341
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 247
Effective length of database: 4,077,219
Effective search space: 1007073093
Effective search space used: 1007073093
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 (21.8 bits)
S2: 58 (25.9 bits)