RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 016811
(382 letters)
>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif,
RNA-modifying enzyme, lyase; 1.50A {Escherichia coli}
SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A
Length = 264
Score = 294 bits (755), Expect = 3e-99
Identities = 87/298 (29%), Positives = 123/298 (41%), Gaps = 54/298 (18%)
Query: 58 QRYLIAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNV 117
+ + +EY G+++ G Q+Q R+V LE+A + +P+++ + RTDAGVH V
Sbjct: 4 YKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQV 63
Query: 118 CHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQER 177
H + + VN L DI V V+ VP DFHARF A R
Sbjct: 64 VHFETTA-----------LRKDAAWTLGVNANLPG--DIAVRWVKTVPDDFHARFSATAR 110
Query: 178 TYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPI 237
Y Y I + H E LD M A + L+G +DF+SFRA CQ+ +P
Sbjct: 111 RYRYIIYNHRLR-PAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPW 169
Query: 238 RTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIAR 297
R + ++V+ G V V +
Sbjct: 170 RNVMHINVTRH------------------------------GPYV----------VVDIK 189
Query: 298 ARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKYD 355
A +F++H VR IVG L VG S + +L AK T A+ A A GL L V Y
Sbjct: 190 ANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYP 247
>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural
NPPSFA, national project on protein structural and
function analyses; 2.25A {Thermus thermophilus}
Length = 249
Score = 279 bits (717), Expect = 1e-93
Identities = 98/303 (32%), Positives = 124/303 (40%), Gaps = 56/303 (18%)
Query: 58 QRYLIAVEYIGTRFSGSQKQLN-CRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASN 116
+R L+ EY GT F+G Q+Q RTV G LE A P +++ + RTDAGVHA +
Sbjct: 2 RRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKAVA-AGRTDAGVHALAM 60
Query: 117 VCHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQE 176
HVDVE V A+N L D+ V R V DFHAR A
Sbjct: 61 PFHVDVES-----------AIPVEKVPEALNRLLPE--DLKVVGAREVAPDFHARKDALW 107
Query: 177 RTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSP 236
R Y YRIL P P S + RA V LDL AM+EA +L+G H+F F +
Sbjct: 108 RAYRYRILVRPHP-SPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGER 166
Query: 237 IRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIA 296
L V+E + +
Sbjct: 167 ELLEARLQVAE--------------------------------------GEAGLEVRLYF 188
Query: 297 RARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKYDL 356
R +SFL QVR +VG L VG G+ ++ ILK A P APA GL Y
Sbjct: 189 RGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAAY-- 246
Query: 357 PED 359
PE+
Sbjct: 247 PEE 249
>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 = 62.6 bits (151), Expect = 1e-10
Identities = 61/354 (17%), Positives = 110/354 (31%), Gaps = 79/354 (22%)
Query: 71 FSGSQKQLNCRTVVGVLEEAFHK-FIGQPVSISLSSRTDAGVHAASNVCHV-----DVER 124
F + Q + ++ V E+AF F + V S + + + H+ V
Sbjct: 9 FETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKS-----ILSKEEIDHIIMSKDAVSG 63
Query: 125 ISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCV---PSDFHARFRAQ-ERTYF 180
+ L +V++ V L+ +++ ++ PS + Q +R Y
Sbjct: 64 T--LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY- 120
Query: 181 YRILSGPEPLSVFEKDRAWHVTEELDLRA----MQEACKVLV----GCHDFSSFRASGCQ 232
+ + F K + L LR ++ A VL+ G + C
Sbjct: 121 ----NDNQV---FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK-TWVALDVCL 172
Query: 233 ANSPIRTLDELHVSEV--VSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNV-FGIRKKH 289
+ +D ++ ++ + N VL + PN S K
Sbjct: 173 SYKVQCKMD----FKIFWLN---LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225
Query: 290 RSYEVIARARSFLYHQVR---LIV-------GVLKA--------VGTGELTVSDVERILK 331
R + + A R L + L+V A + T V+D
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285
Query: 332 AKTVT---AASPMAPACGLSLGFVKY------DLPEDDQTDAAESLETCPDPVS 376
++ + + P SL +KY DLP E L T P +S
Sbjct: 286 TTHISLDHHSMTLTPDEVKSL-LLKYLDCRPQDLPR-------EVLTTNPRRLS 331
Score = 38.7 bits (89), Expect = 0.003
Identities = 50/344 (14%), Positives = 90/344 (26%), Gaps = 118/344 (34%)
Query: 44 TR--TVTEVMSTNKRIQRYLIAVEYIGTRFSGSQ------KQLNCRTVVGVL-EEAFHKF 94
TR VT+ +S I++++ + + K L+CR L E
Sbjct: 272 TRFKQVTDFLSAATTTH---ISLDHHSMTLTPDEVKSLLLKYLDCR--PQDLPREV-LT- 324
Query: 95 IGQPVSISL-SSRTDAGVHAASNVCHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSE 153
P +S+ + G+ N HV+ ++++ ++ ++N L+
Sbjct: 325 -TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT-------------IIESSLNV-LE-- 367
Query: 154 GDIMVTDVRCVPSDFHARFRAQERTYFYRILSGPEPLSVFEKD---------RAWHVTEE 204
P+++ F LSVF W +
Sbjct: 368 -----------PAEYRKMFDR---------------LSVFPPSAHIPTILLSLIWFDVIK 401
Query: 205 LDLRAMQEAC--KVLVGCHDF-SSFRASGCQ--ANSPIRTLDELHVSEVVSTALFSSINQ 259
D+ + LV S+ + LH S V + + +
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461
Query: 260 DSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARARSFLYHQVRLIVGVLKAVGTG 319
D + +D Y I +H LK +
Sbjct: 462 DDLIPPYLDQY--------------------FYSHIG------HH--------LKNIEHP 487
Query: 320 ELTVS------DVERILKAK---TVTAASPMAPACGLSLGFVKY 354
E D R L+ K TA + Y
Sbjct: 488 ERMTLFRMVFLDF-RFLEQKIRHDSTAWNASGSILNTLQQLKFY 530
>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 = 48.9 bits (116), Expect = 2e-06
Identities = 60/411 (14%), Positives = 107/411 (26%), Gaps = 147/411 (35%)
Query: 15 ASKIPEEKEEDHQNDSVEEEEEYPEEVPETRTVTEVMSTNKRIQRYLIAVEYIGTRFSGS 74
+PE E +D E T E++ ++L Y+ + S
Sbjct: 38 NKILPEPTEGFAADD-------------EPTTPAELVG------KFL---GYVSSLVEPS 75
Query: 75 QKQLNC---RTVVGVLEEAF------HKFIGQPVSISLSSRTDAGVHAASNV--CHVDVE 123
+ + E + H L D + + ++
Sbjct: 76 KVGQFDQVLNLCLTEFENCYLEGNDIHALAA-----KLLQENDTTLVKTKELIKNYITAR 130
Query: 124 RISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQ--ERTYF- 180
++KR +S++ R EG+ + A F Q YF
Sbjct: 131 IMAKRPFD---KKSNSALFRAV------GEGN----------AQLVAIFGGQGNTDDYFE 171
Query: 181 --------YRILSGP---------EPLSVFEKDRAWHVTEELDLRA-MQEA--------- 213
Y +L G L D T+ L++ ++
Sbjct: 172 ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYL 231
Query: 214 --CKV---LVG----CHDFSSFRASGCQANSPIRTLDEL-----HVSEVVSTALFSSINQ 259
+ L+G H + + G +P L H +V+ +
Sbjct: 232 LSIPISCPLIGVIQLAHYVVTAKLLGF---TPGELRSYLKGATGHSQGLVTAVAIAE--- 285
Query: 260 DSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARARSFLYHQVRLIVGV--LKAVG 317
+ S F + + +A + L+ +GV +A
Sbjct: 286 ------TDSWES-----------F--------FVSVRKAITVLFF-----IGVRCYEAYP 315
Query: 318 TGELTVSDVERILKAKTVTAASPMAPACGLSLGFV-KY------DLPEDDQ 361
L S +E L+ SPM L+ V Y LP Q
Sbjct: 316 NTSLPPSILEDSLEN-NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
Score = 45.4 bits (107), Expect = 2e-05
Identities = 51/353 (14%), Positives = 101/353 (28%), Gaps = 92/353 (26%)
Query: 86 VLEEAFHKFIGQPV-SISLSSRTDAGVH-AASNVCHVDVERISKRKPGEVLPPHDSSVVR 143
L+E F+K + +P + + +V S +P +V V+
Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVS----SLVEPSKV--GQFDQVLN 85
Query: 144 RAVNHFLQSEGDIMV-TDVRCV----PSDFHARFRAQE---RTYFYRILSGPEPLSVFEK 195
+ F E + D+ + + + + Y + P
Sbjct: 86 LCLTEF---ENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN 142
Query: 196 DRAWHVTEELDLRAMQE-ACKVLVGCHDFSSFRASGCQANSPIRTLDEL----HVSEVVS 250
L RA+ E ++ + F G Q N+ +EL V+
Sbjct: 143 SA-------L-FRAVGEGNAQL------VAIF---GGQGNT-DDYFEELRDLYQTYHVLV 184
Query: 251 TALFSSINQD-SPVLSSIDNSSKL---GMPNGGSNVFG-IRKKHR--SYEVIARAR-SF- 301
L + S ++ + ++ K+ G+ N+ + + + S
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGL-----NILEWLENPSNTPDKDYLLSIPISCP 239
Query: 302 ---LYHQVRLIVGVLKAVGTGELTVSDVERILKAKT-----VTAASPMAPA--------- 344
+ +V K +G T ++ LK T + A +A
Sbjct: 240 LIGVIQLAHYVV-TAKLLG---FTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS 295
Query: 345 ----------CGL--SLGFVKYDLPEDDQTDAAESLETCPDP---VSRKRRLQ 382
G+ + LP D+ E+ E P P +S + Q
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQ 348
Score = 31.2 bits (70), Expect = 0.82
Identities = 26/147 (17%), Positives = 45/147 (30%), Gaps = 47/147 (31%)
Query: 233 ANSPI-RTL-DE--LHVSEVVSTALFSSINQDSPVLSSI--DNSSKLGMPNGGSNVFGIR 286
S + + + H + FS + I +N L + GG IR
Sbjct: 1637 KTSKAAQDVWNRADNHFKDTYG---FS--------ILDIVINNPVNLTIHFGGEKGKRIR 1685
Query: 287 KKHRS--YEVIARARSFLYHQVRLIV------------GVLK-------AVGTGELTVSD 325
+ + + +E I + + I G+L A+ +
Sbjct: 1686 ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL----TLMEK 1741
Query: 326 -VERILKAKTVT-AASPMAPACGLSLG 350
LK+K + A + A G SLG
Sbjct: 1742 AAFEDLKSKGLIPADATFA---GHSLG 1765
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.1 bits (72), Expect = 0.21
Identities = 9/59 (15%), Positives = 22/59 (37%), Gaps = 18/59 (30%)
Query: 3 EFAKRISECSEQASKIPEE------KEED----HQNDSVE--------EEEEYPEEVPE 43
E KR+ E + + +E K+ + Q++ VE ++ + ++
Sbjct: 93 EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDA 151
Score = 27.4 bits (60), Expect = 6.5
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 12/65 (18%)
Query: 5 AKRISECSEQASKIPEEKEED-HQNDSVEEEEEYPEEVPE---------TRTVTEVMSTN 54
A R+++ E K EE+ + + D+ + E +E E + +E + N
Sbjct: 77 ADRLTQEPESIRKWREEQRKRLQELDAASKVME--QEWREKAKKDLEEWNQRQSEQVEKN 134
Query: 55 KRIQR 59
K R
Sbjct: 135 KINNR 139
>3bmx_A Uncharacterized lipoprotein YBBD; beta-N-hexosaminidase, TIM
barrel, glycos hydrolase, membrane, palmitate; HET: P4G;
1.40A {Bacillus subtilis} PDB: 3cqm_A* 3nvd_A* 3lk6_A*
Length = 642
Score = 27.6 bits (61), Expect = 8.3
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 305 QVRLIVGVLKAVGTGELTVSD----VERILKAK 333
R+I + +AV G++ VERI+ K
Sbjct: 361 FARVIQALKEAVKNGDIPEQQINNSVERIISLK 393
>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine
hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1
c.40.1.1
Length = 349
Score = 27.1 bits (61), Expect = 9.7
Identities = 5/21 (23%), Positives = 13/21 (61%)
Query: 138 DSSVVRRAVNHFLQSEGDIMV 158
DS+++R+ + + S D+ +
Sbjct: 11 DSALMRQIMTEIINSHSDMEM 31
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
0.316 0.131 0.374
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,793,677
Number of extensions: 350215
Number of successful extensions: 682
Number of sequences better than 10.0: 1
Number of HSP's gapped: 669
Number of HSP's successfully gapped: 23
Length of query: 382
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 287
Effective length of database: 4,049,298
Effective search space: 1162148526
Effective search space used: 1162148526
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)