RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1424
(305 letters)
>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 = 47.4 bits (112), Expect = 5e-06
Identities = 57/314 (18%), Positives = 92/314 (29%), Gaps = 141/314 (44%)
Query: 12 VRGTNPQYL----------IEKIIRAR-IYDSKYWKEECFALSAELLVDKAME-LRYIG- 58
+ G P L + ++ A I ++ W+ S + V KA+ L +IG
Sbjct: 255 LLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE------SFFVSVRKAITVLFFIGV 308
Query: 59 ---GVF---------------GGNIKPTPFLCLILKMLQIQ-PEKDIVVEFIK--NEEF- 96
+ P+P ML I ++ V +++ N
Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPSP-------MLSISNLTQEQVQDYVNKTNSHLP 361
Query: 97 --KYVR-AL--GAYYMRLTGSSVDCY---KYLEPLFADS-----------RKLRFQNR-- 135
K V +L GA + ++G Y L A S RKL+F NR
Sbjct: 362 AGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL 421
Query: 136 -----------QGAFEVIHMDEYIDQL-------------------LRE------ERMCD 159
A ++I+ D + + LR ER+ D
Sbjct: 422 PVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVD 481
Query: 160 VIL------PRIQK---RHVLEENNEIEVKVSILDDDIDDGGSSSSED---ENEE----- 202
I+ + H+L D GG+S N++
Sbjct: 482 CIIRLPVKWETTTQFKATHIL---------------DFGPGGASGLGVLTHRNKDGTGVR 526
Query: 203 ---AGEVYDKNRMD 213
AG + D N D
Sbjct: 527 VIVAGTL-DINPDD 539
Score = 28.1 bits (62), Expect = 5.0
Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 19/77 (24%)
Query: 7 KDAKSVRGTNPQYLIEKIIRARIYDSKYWKEECFALSA--------------ELLVDKAM 52
D + + G+ + +++ IIR + W E A +L +
Sbjct: 466 SDLRVLSGSISERIVDCIIRLPV----KW-ETTTQFKATHILDFGPGGASGLGVLTHRNK 520
Query: 53 ELRYIGGVFGGNIKPTP 69
+ + + G + P
Sbjct: 521 DGTGVRVIVAGTLDINP 537
>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 = 46.0 bits (108), Expect = 1e-05
Identities = 48/278 (17%), Positives = 79/278 (28%), Gaps = 61/278 (21%)
Query: 10 KSVRGTNPQYLIEKIIRARIYD----SKYWK-------EECFALSAELLVDKAMELRYIG 58
+ V TNP+ L II I D WK S +L +
Sbjct: 320 REVLTTNPRRL--SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDR 377
Query: 59 -GVFGGNIK-PTPFLCLI-LKMLQIQPEKDIVVEFIK-------NEEFKYVRALGAYYMR 108
VF + PT L LI +++ +V + K +E ++ + Y+
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVM-VVVNKLHKYSLVEKQPKESTI--SIPSIYLE 434
Query: 109 LTGSSVDCYKYLEPLFADSRKLRFQNRQGAFEVIHMDEYI--------DQLLREERMCDV 160
L + L D + ++D+Y + ERM
Sbjct: 435 LKVKLEN-EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF 493
Query: 161 ILPRIQKRHVLEENNEIEVKVSILDDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSS 220
R V + +E K I D S S + +
Sbjct: 494 -------RMVFLDFRFLEQK--IRHDSTAWNASGSILN-----------TLQQLK----- 528
Query: 221 KYDSHHRDPDKERDRRYRSEKSTKERVRERS-RSKERD 257
Y + D D + +R + ++ E SK D
Sbjct: 529 FYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTD 566
Score = 37.1 bits (85), Expect = 0.007
Identities = 26/231 (11%), Positives = 72/231 (31%), Gaps = 50/231 (21%)
Query: 70 FLCLILKMLQIQPEKDIVVEFIKNEEFKYV-----RALGAYYM----RLTGSSVDCYKYL 120
F + + +D+ + EE ++ G + + K++
Sbjct: 25 FEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM-VQKFV 83
Query: 121 EPLFADS-----RKLRFQNRQGAFEVIHMDEYIDQLLREERMCDVILPRIQKRHV--LEE 173
E + + ++ + RQ + YI+Q +R+ + K +V L+
Sbjct: 84 EEVLRINYKFLMSPIKTEQRQPSMM---TRMYIEQR---DRLYNDN-QVFAKYNVSRLQP 136
Query: 174 NNEIEVKVSILDDDID-----DGGS----------SSSEDENEEAGEVYDKNRMDVDTYH 218
++ + L + GS S + + + +++ +++ +
Sbjct: 137 YLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF---WLNLKNCN 193
Query: 219 SSKYD-------SHHRDPD-KERDRRYRSEKSTKERVRERSRSKERDRRHR 261
S + + DP+ R + K ++ R + + +
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244
Score = 35.2 bits (80), Expect = 0.029
Identities = 37/328 (11%), Positives = 91/328 (27%), Gaps = 89/328 (27%)
Query: 3 NRTVKDA-KSVRGTNPQYLIEKIIRARIYDSKYWKEECF--ALSAELLVDKAMELRYIGG 59
V+ + V N ++L+ K E ++ + +++ L
Sbjct: 76 EEMVQKFVEEVLRINYKFLMSP-----------IKTEQRQPSMMTRMYIEQRDRLYNDNQ 124
Query: 60 VFG-GNI-KPTPFLCLILKMLQIQPEKDIVV-------------EFIKNEEFKYVRALGA 104
VF N+ + P+L L +L+++P K++++ + + + +
Sbjct: 125 VFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184
Query: 105 YYMRL--TGSSVDCYKYLEPLFADSRKLRFQNRQGAFEVIHMDEYIDQLLREERMCDVIL 162
+++ L S + L+ L + + I LR ++
Sbjct: 185 FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR-----RLLK 239
Query: 163 PRIQKRHVLEENNEIEVKVSILDDDIDDGGSSSSEDENEEAGEVYDKN---------RMD 213
+ + +L +L + V + ++
Sbjct: 240 SKPYENCLL-----------VLLN-------------------VQNAKAWNAFNLSCKIL 269
Query: 214 VDTYHSSKYDS----HHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSK--SPRH 267
+ T D + + K + + + +D +PR
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329
Query: 268 ------KDRDY-DR-DRYKDYEREKYRS 287
RD D +K +K +
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTT 357
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 39.4 bits (91), Expect = 0.001
Identities = 27/180 (15%), Positives = 50/180 (27%)
Query: 126 DSRKLRFQNRQGAFEVIHMDEYIDQLLREERMCDVILPRIQKRHVLEENNEIEVKVSILD 185
D R + E ++ ++ + R + R + + E + +
Sbjct: 220 DERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRE 279
Query: 186 DDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTKE 245
D ++ R + D D E
Sbjct: 280 RSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDG 339
Query: 246 RVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRHR 305
+ ++RDR R ++R DRDR +D +RE R +R RD +
Sbjct: 340 PDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQ 399
Score = 39.1 bits (90), Expect = 0.001
Identities = 23/120 (19%), Positives = 37/120 (30%)
Query: 186 DDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTKE 245
DD D+ R + + R RR + +E
Sbjct: 214 DDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEE 273
Query: 246 RVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRHR 305
R R R RSK++DR + +S R ++R K+ R + + D D
Sbjct: 274 RRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPG 333
Score = 37.5 bits (86), Expect = 0.004
Identities = 26/121 (21%), Positives = 41/121 (33%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
D D S E A ++ S D +
Sbjct: 281 SKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGP 340
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRH 304
+ E+ R ++R+RR +S R + RD DRDR +D E ++ +RG RG +
Sbjct: 341 DGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQD 400
Query: 305 R 305
Sbjct: 401 N 401
Score = 36.4 bits (83), Expect = 0.010
Identities = 20/121 (16%), Positives = 34/121 (28%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
+ + + M + + D E+ +
Sbjct: 289 KRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGR 348
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRH 304
+R RER RS +R R R +DRD + R + R G +D G +
Sbjct: 349 DRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGN 408
Query: 305 R 305
Sbjct: 409 D 409
Score = 36.4 bits (83), Expect = 0.011
Identities = 26/121 (21%), Positives = 36/121 (29%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
D D S S E E + D S+ D + +
Sbjct: 285 DRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPE 344
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRH 304
E+ R+R R + R R + R +DRD DRDR RD G +
Sbjct: 345 EKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLE 404
Query: 305 R 305
Sbjct: 405 G 405
Score = 36.0 bits (82), Expect = 0.013
Identities = 25/211 (11%), Positives = 56/211 (26%)
Query: 95 EFKYVRALGAYYMRLTGSSVDCYKYLEPLFADSRKLRFQNRQGAFEVIHMDEYIDQLLRE 154
E+++ R + + Y G +D + L + ++ R+ + +
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIR 209
Query: 155 ERMCDVILPRIQKRHVLEENNEIEVKVSILDDDIDDGGSSSSEDENEEAGEVYDKNRMDV 214
D ++ + + + + +
Sbjct: 210 HSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSR 269
Query: 215 DTYHSSKYDSHHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDR 274
D + +D D++R RR + R RER ++ D D
Sbjct: 270 DKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDD 329
Query: 275 DRYKDYEREKYRSDRDRGDRRDRGDRDRRHR 305
+ + ++G RDR R
Sbjct: 330 GPPGELGPDGPDGPEEKGRDRDRERRRSHRS 360
Score = 36.0 bits (82), Expect = 0.014
Identities = 16/121 (13%), Positives = 31/121 (25%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
+ + G E EAG+ + + + D++R+RR +
Sbjct: 304 ERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERE 363
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRH 304
R R + + RD R + D D + +
Sbjct: 364 RRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGY 423
Query: 305 R 305
Sbjct: 424 L 424
Score = 35.2 bits (80), Expect = 0.025
Identities = 14/121 (11%), Positives = 25/121 (20%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
+ E G + PD + +
Sbjct: 293 SRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDR 352
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDRDRRH 304
ER R +ER R R ++ + E + + + D R
Sbjct: 353 ERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRD 412
Query: 305 R 305
Sbjct: 413 M 413
Score = 34.1 bits (77), Expect = 0.047
Identities = 12/116 (10%), Positives = 31/116 (26%)
Query: 185 DDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTK 244
D + + + ++ GE+ + + R ER+RR ++
Sbjct: 314 GDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRD 373
Query: 245 ERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSDRDRGDRRDRGDR 300
+ + +R +D + + R+ Y +
Sbjct: 374 RDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENG 429
>3v97_A Ribosomal RNA large subunit methyltransferase L; YCBY, RNA
methyltransferase, ribosome RNA, SAH, RLML; HET: SAH
OSU; 2.20A {Escherichia coli} PDB: 3v8v_A*
Length = 703
Score = 28.1 bits (63), Expect = 3.9
Identities = 13/92 (14%), Positives = 23/92 (25%), Gaps = 6/92 (6%)
Query: 211 RMDVDTYHSSKYDSHHRDPDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDR 270
+D + +S Y + + E+ +E +R +
Sbjct: 370 PLDCVQKNYHVAESTPDSKPAMVAEDYTNRLRKNLKKFEKWARQEGIECYRLYDADLPEY 429
Query: 271 DYDRDRYKD------YEREKYRSDRDRGDRRD 296
+ DRY D Y K R
Sbjct: 430 NVAVDRYADWVVVQEYAPPKTIDAHKARQRLF 461
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 27.4 bits (60), Expect = 4.1
Identities = 8/55 (14%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 230 DKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREK 284
+ E R++R E+ ++R++E + + + KD + + + +
Sbjct: 83 EPESIRKWREEQ--RKRLQELD-AASKVMEQEWREKAKKDLE---EWNQRQSEQV 131
Score = 26.7 bits (58), Expect = 9.3
Identities = 5/44 (11%), Positives = 15/44 (34%), Gaps = 8/44 (18%)
Query: 230 DKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYD 273
K+ + + + E+ + +R ++ + D D
Sbjct: 117 KKDLEEWNQRQSEQVEKNKINNRIADKAFY--------QQPDAD 152
>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system,
helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP;
2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*
Length = 1038
Score = 28.0 bits (62), Expect = 4.6
Identities = 19/171 (11%), Positives = 55/171 (32%), Gaps = 2/171 (1%)
Query: 119 YLEPLFADSRKLRFQNRQGAFEVIHMDEYIDQLLREERMCDVILPRIQKRHVLEENNEIE 178
Y E + + + A E + Y+D E + + + N+I
Sbjct: 795 YDEFATLKALQQIDLSDPVAVEKFKAEHYVDDEKFAELQTIRLPADRKIQDYRSAYNDIR 854
Query: 179 VKVSILDDDIDDGGSSSSEDENEEAGEVYDKNRMDVDTYHSSKYDSHHRDPDKERDRRYR 238
+ S++ D+ ++ +++D Y H+R + +
Sbjct: 855 DWQRREKEAEKKEKSTTDWDDVVFEVDLLKSQEINLD-YILGLIFEHNRQNKGKGEMIEE 913
Query: 239 SEKSTKERVRERSRSKE-RDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSD 288
++ + + R++ D ++ D+ D + + + + + +
Sbjct: 914 VKRLIRSSLGNRAKEGLVVDFIQQTNLDDLPDKASIIDAFFTFAQREQQRE 964
>3u5c_H RP30, RP40, 40S ribosomal protein S7-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3u5g_H
Length = 190
Score = 27.0 bits (59), Expect = 6.9
Identities = 3/76 (3%), Positives = 14/76 (18%), Gaps = 2/76 (2%)
Query: 229 PDKERDRRYRSEKSTKERVRERSRSKERDRRHRSKSPRHKDRDYDRDRYKDYEREKYRSD 288
+ S + + K + + + + + +
Sbjct: 21 AQAFVELENSS--PELKAELRPLQFKSIREIDVAGGKKALAIFVPVPSLAGFHKVQTKLT 78
Query: 289 RDRGDRRDRGDRDRRH 304
R+ +
Sbjct: 79 RELEKKFQDRHVIFLA 94
>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 = 26.6 bits (58), Expect = 8.8
Identities = 9/64 (14%), Positives = 19/64 (29%), Gaps = 20/64 (31%)
Query: 243 TKERVRERSRSKERDRRHRSKSPRHKDR------DYDR-------------DRYKDYERE 283
T+E + +R+ + + P K + D+ D E
Sbjct: 3 TRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSE 62
Query: 284 KYRS 287
+R+
Sbjct: 63 -WRT 65
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
0.318 0.137 0.394
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: 4,907,704
Number of extensions: 304664
Number of successful extensions: 954
Number of sequences better than 10.0: 1
Number of HSP's gapped: 847
Number of HSP's successfully gapped: 52
Length of query: 305
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 212
Effective length of database: 4,105,140
Effective search space: 870289680
Effective search space used: 870289680
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 (21.7 bits)
S2: 57 (26.5 bits)