RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13052
(533 letters)
>1srq_A RAP1GAP, GTPase-activating protein 1; mixed alpha-beta, signaling
protein; 2.90A {Homo sapiens} SCOP: e.55.1.1 PDB:
3brw_A*
Length = 341
Score = 364 bits (935), Expect = e-123
Identities = 190/343 (55%), Positives = 245/343 (71%), Gaps = 4/343 (1%)
Query: 65 PTAPWRSKIECDDTAKCYRRFFLGREHSNFVGVDNELGPVLLSTKTELVGNQSHTRLLLR 124
PT + K+EC+ TA+ YR+ FLG+EH N+ +D LG ++ S K +++G+Q H RLLLR
Sbjct: 1 PT--TKVKLECNPTARIYRKHFLGKEHFNYYSLDTALGHLVFSLKYDVIGDQEHLRLLLR 58
Query: 125 LKTGTVHELLPPNC--ANASPQTMARLVNEQLTCSSLTPVLCPQASSLIAAYDEHVLVSQ 182
K T H+++P +C + MA+LV E + PVL P+AS LI +DEHV+ +
Sbjct: 59 TKCRTYHDVIPISCLTEFPNVVQMAKLVCEDVNVDRFYPVLYPKASRLIVTFDEHVISNN 118
Query: 183 FKFGVLYQRHGQITEEELFANKHTSPAFDQFLNLLGQRILLKDHKGYRGGLDTQFRQTGE 242
FKFGV+YQ+ GQ +EEELF+ SPAF +FL LGQ++ L+D KG+RGGLD QTG
Sbjct: 119 FKFGVIYQKLGQTSEEELFSTNEESPAFVEFLEFLGQKVKLQDFKGFRGGLDVTHGQTGT 178
Query: 243 QAVYQVFKEREIMFHVSTLLPFTENDPQQLQRKRHIGNDIVAIVFQETNTPFSPDMIASH 302
++VY F+ +EIMFHVST LP+TE D QQLQRKRHIGNDIVA+VFQ+ NTPF PDMIAS+
Sbjct: 179 ESVYCNFRNKEIMFHVSTKLPYTEGDAQQLQRKRHIGNDIVAVVFQDENTPFVPDMIASN 238
Query: 303 FLHAFIVVQVIDPNTPNTRYKVSVTARDDVPFFGPNFPQPAIFRADSDFKEFLLTKLINA 362
FLHA++VVQ YKVSVTARDDVPFFGP P PA+FR +F+EFLLTKLINA
Sbjct: 239 FLHAYVVVQAEGGGPDGPLYKVSVTARDDVPFFGPPLPDPAVFRKGPEFQEFLLTKLINA 298
Query: 363 ENAAYKAHKFAKLELRTRSSLLHSLCEELKEKTREFLGGEGED 405
E A YKA KFAKLE RTR++LL +L EEL ++ +G G++
Sbjct: 299 EYACYKAEKFAKLEERTRAALLETLYEELHIHSQSMMGLGGDE 341
Score = 57.9 bits (139), Expect = 2e-09
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 421 FIDTEHSNFVGVDNELGPVLLSTKTELVGNQSHTRLLLRLKTGTVHELLPPNCANASPQT 480
F+ EH N+ +D LG ++ S K +++G+Q H RLLLR K T H+++P +C P
Sbjct: 20 FLGKEHFNYYSLDTALGHLVFSLKYDVIGDQEHLRLLLRTKCRTYHDVIPISCLTEFP-- 77
Query: 481 MARLRTRSSLLHSLCEELKEKT 502
+ +CE++
Sbjct: 78 -----NVVQMAKLVCEDVNVDR 94
Score = 34.4 bits (78), Expect = 0.086
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 485 RTRSSLLHSLCEELKEKTREFLGGEGED 512
RTR++LL +L EEL ++ +G G++
Sbjct: 314 RTRAALLETLYEELHIHSQSMMGLGGDE 341
>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 = 61.4 bits (148), Expect = 5e-10
Identities = 63/417 (15%), Positives = 117/417 (28%), Gaps = 95/417 (22%)
Query: 23 LLEETLRGSLPYPMIVTPPSGGYWLD-GYENESR-----------QNSNSHQHGPTAPWR 70
+ + Y + +WL+ N Q +
Sbjct: 166 VALDVCL---SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
Query: 71 SKIECDDTAKCYRRFFLGREHSN--FVGVDN----------ELG-PVLLSTK----TELV 113
K+ RR + + N V + N L +LL+T+ T+ +
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENCLLV-LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL 281
Query: 114 GNQSHTRL----------------LLRLKTGTVHELLPPNCANASPQTMA---------- 147
+ T + LL + LP +P+ ++
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL 341
Query: 148 -RLVN-EQLTCSSLTPVLCPQASSLIAAYDEHVLVSQFKFGVLYQRHGQITEE--ELFAN 203
N + + C LT ++ ++S + + F ++ I L
Sbjct: 342 ATWDNWKHVNCDKLTTII--ESS--LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397
Query: 204 KHTSPAFDQFLNLLGQRILL-KDHKGYRGGLDTQFRQTGEQAVYQVFKEREIMFHVSTLL 262
+N L + L+ K K + + + + + + R I+ H +
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK 457
Query: 263 PFTENDPQQLQRKR----HIGNDIVAIVFQETNTPFSPDMIASHFLHAFIVVQVIDPNTP 318
F +D + HIG+ + I E T F + FL I N
Sbjct: 458 TFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNAS 517
Query: 319 ----NT-----RYKVSVTARDDVPFFGPNFPQPAIFRADSDFKEFLL---TKLINAE 363
NT YK P+ N P+ R + +FL LI ++
Sbjct: 518 GSILNTLQQLKFYK---------PYICDNDPKYE--RLVNAILDFLPKIEENLICSK 563
Score = 42.5 bits (99), Expect = 3e-04
Identities = 47/369 (12%), Positives = 98/369 (26%), Gaps = 114/369 (30%)
Query: 234 DTQFRQTGEQAVYQVFKEREIMFHVSTLLPFTENDPQQLQRKRHI-------GNDIVAIV 286
+ + + + + E + ++ + + ++V
Sbjct: 32 NFDCKDV-QDMPKSILSKEE----IDHII----MSKDAVSGTLRLFWTLLSKQEEMVQKF 82
Query: 287 FQETNTPFSPDMIASHFLHAFIVVQVIDPNTPNTRYKVSVTARD----DVPFFGP-NFPQ 341
+E + FL + I + P+ Y + RD D F N +
Sbjct: 83 VEEV---LRINY---KFLMSPIKTEQRQPSMMTRMY---IEQRDRLYNDNQVFAKYNVSR 133
Query: 342 PAIFRADSDFKEFLLTKLINAEN----------------AAYKAHKFAK--------LEL 377
+ ++ LL +L A+N ++K L L
Sbjct: 134 LQPYLK---LRQALL-ELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNL 189
Query: 378 RTRSS------LLHSLC---------------------EELKEKTREFLGGEG------- 403
+ +S +L L ++ + R L +
Sbjct: 190 KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249
Query: 404 ----EDTRHGDTSNGS----GTGTRFIDTEHSNFVGVDNELGPVLLSTKTELVGNQSHTR 455
++ + + N S T TR + ++F+ L L +
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLT-TR--FKQVTDFLSAATTTHISLDHHSMTL--TPDEVK 304
Query: 456 LLLRLKTGTVHELLPPNCANASPQTM----ARLR----TRSSLLHSLCEELKEKTREFLG 507
LL + LP +P+ + +R T + H C++L L
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364
Query: 508 G-EGEDTRH 515
E + R
Sbjct: 365 VLEPAEYRK 373
Score = 36.8 bits (84), Expect = 0.022
Identities = 33/249 (13%), Positives = 73/249 (29%), Gaps = 72/249 (28%)
Query: 313 IDPNTPNTRYKVSVTARDDVPFFGPNFPQPAIFRADSDFKEFLLTK-----LINAENAAY 367
+D T +Y+ +D + F F + D + +L+K +I +++A
Sbjct: 7 MDFETGEHQYQY----KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVS 62
Query: 368 KAHKFAKLELRTRSSLLHSLCEELKEKTREFLGGEGEDTRHGDTSNGSGTGTRFIDT--- 424
+ L + ++ EE+ +FL + S +I+
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFL----MSPIKTEQRQPSMMTRMYIEQRDR 118
Query: 425 -----------------------------EHSNFVGVDNELG--------PVLLSTKTEL 447
+ V +D LG V LS K +
Sbjct: 119 LYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC 178
Query: 448 ----------VGNQSHTRLLLRLKTGTVHELLPPNCANASPQTMARLRTRSSLLHSLCEE 497
+ N + +L + ++++ P + + + +LR
Sbjct: 179 KMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI---------HS 229
Query: 498 LKEKTREFL 506
++ + R L
Sbjct: 230 IQAELRRLL 238
>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 = 59.7 bits (144), Expect = 2e-09
Identities = 102/605 (16%), Positives = 186/605 (30%), Gaps = 183/605 (30%)
Query: 27 TLR------GSLPYPMIVTPPSGGYWLDGYENESRQNSNSHQHGPTAPWRSKIECDDTAK 80
+ R GSL + ++V P+ ++ ++ ++ N PT + + E A+
Sbjct: 5 STRPLTLSHGSLEHVLLV--PTASFF---IASQLQEQFNKILPEPTEGFAADDEPTTPAE 59
Query: 81 CYRRFFLGREHSNFVGVDNELGPVLLSTKTELVGNQSHTRLLLR------LKTGTVHEL- 133
+F LG +V + + P + +++ L L L+ +H L
Sbjct: 60 LVGKF-LG-----YV--SSLVEPSKVGQFDQVL------NLCLTEFENCYLEGNDIHALA 105
Query: 134 --LPPNCANASPQTMARLVN--EQLTCSSLTPVLCPQASSLI-AAYDEHV-LVSQFKFGV 187
L +T + N + P S+L A + + LV+ F G
Sbjct: 106 AKLLQENDTTLVKTKELIKNYITARIMAK-RPFDKKSNSALFRAVGEGNAQLVAIF--G- 161
Query: 188 LYQRHGQ-ITEE------ELFANKHTSPAF-DQFLNLLGQRI--LLKDH----KGYRGGL 233
GQ T++ +L+ T + + + L++ K + GL
Sbjct: 162 -----GQGNTDDYFEELRDLY---QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL 213
Query: 234 D-----------------------------TQFRQTGEQAVYQVFKEREIMFHVSTLLPF 264
+ Q A Y V +
Sbjct: 214 NILEWLENPSNTPDKDYLLSIPISCPLIGVIQL------AHYVVT------AKLLGF--- 258
Query: 265 TENDPQQLQRKRH----IGNDIV-AIVFQETNTPFSPDMIASHFLHA--FIVVQVIDPNT 317
P +L+ +V A+ ET++ S + + FI V+ +
Sbjct: 259 ---TPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYE-AY 314
Query: 318 PNTRYKVSVTARDDVPFFGPNFPQP--AIFRADSDFKEFLLTKLINAENAAYKAHKFAKL 375
PNT + + +D P P +I S+ + + +N N+ A K ++
Sbjct: 315 PNTS--LPPSILEDSLENNEGVPSPMLSI----SNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 376 ELR-TRSSL--------LHSLCEELKEKTREFLGGEGED-TRHGDTSNGSGTGTRF--ID 423
L +L L+ L L R+ G D +R + RF +
Sbjct: 369 SLVNGAKNLVVSGPPQSLYGLNLTL----RKAKAPSGLDQSRIPFSERKLKFSNRFLPVA 424
Query: 424 T-EHSNFVGVDNELGPVLLSTKTELVGNQSHTRLLLR---LKTGTVHELLPPNCANASPQ 479
+ HS+ L P +LV N + ++ V+
Sbjct: 425 SPFHSHL------LVPASDLINKDLVKNN----VSFNAKDIQI-PVY----------DTF 463
Query: 480 TMARLRT-RSSLLHSLCEELK------EKTREFLG------GEGEDTRHGD-TS-NGSGT 524
+ LR S+ + + + E T +F G G + G T N GT
Sbjct: 464 DGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGT 523
Query: 525 GTRFI 529
G R I
Sbjct: 524 GVRVI 528
Score = 55.4 bits (133), Expect = 4e-08
Identities = 76/494 (15%), Positives = 144/494 (29%), Gaps = 137/494 (27%)
Query: 27 TLRGSLPYPMIVTPPSGGYWLDGY-ENESRQNSNSHQHGPTAPWRSKIECDDTAKCYRRF 85
L L T + Y + +A +R+ + A+ F
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAV--GEGNAQLVAIF 160
Query: 86 FLGREHSNFVGVDNELGPVLLSTKTELVGN--QSHTRLLLRLKTGTVH--ELLPPNC--- 138
G + + + EL L T LVG+ + L L T+ ++
Sbjct: 161 --GGQGNTDDYFE-ELRD-LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNIL 216
Query: 139 -----ANASPQTMARLVNEQLTCSSLTPVLCPQASSLIAAYDEHVLVSQF-KFGVLYQRH 192
+ +P ++ S P+ CP LI V Q + V +
Sbjct: 217 EWLENPSNTP-------DKDYLLSI--PISCP----LIG-------VIQLAHYVVTAKLL 256
Query: 193 GQITEEELFANKH----------------TSPAFDQFLNLLGQ--RILLKDHKGYRGGLD 234
G T EL + + +++ F + + +L G R
Sbjct: 257 G-FTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF--FIGVRC--- 310
Query: 235 TQ--FRQTG-EQAVYQVFKEREI-----MFHVS-----TLLPFTENDPQQLQRKRHIGND 281
+ T ++ + E M +S + + L + +
Sbjct: 311 -YEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVE-- 367
Query: 282 IVAIVFQETNTPFSPDMIASHF--------LHAFIVVQV--------IDPN-TPNTRYKV 324
+++V N + L+ + + +D + P + K+
Sbjct: 368 -ISLV----NGA-------KNLVVSGPPQSLYGL-NLTLRKAKAPSGLDQSRIPFSERKL 414
Query: 325 SVTAR---DDVPFFGPNFPQPAIFRADSDFKEFLLTKLINAENAA---YKAHKFAKLELR 378
+ R PF PA + D + ++ NA++ Y F +LR
Sbjct: 415 KFSNRFLPVASPFHSH-LLVPASDLINKDLVKNNVS--FNAKDIQIPVY--DTFDGSDLR 469
Query: 379 T-RSSLLHSLCEELK------EKTREFLG------GEGEDTRHGD-TS-NGSGTGTRFID 423
S+ + + + E T +F G G + G T N GTG R I
Sbjct: 470 VLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIV 529
Query: 424 TEHSNFVGVDNELG 437
+ + D++ G
Sbjct: 530 AGTLD-INPDDDYG 542
Score = 42.3 bits (99), Expect = 5e-04
Identities = 51/312 (16%), Positives = 82/312 (26%), Gaps = 138/312 (44%)
Query: 239 QTGEQAV------YQVFKE-REIMFHVSTLLPFTENDPQQLQRKRHIGNDIVAIVFQETN 291
Q G Q Y+ K +++ + D K G I+ IV
Sbjct: 1624 Q-GSQEQGMGMDLYKTSKAAQDV---------WNRAD---NHFKDTYGFSILDIVIN--- 1667
Query: 292 TPFSPDMIASHF-----------LHAFIVVQVIDPNTPNTRYKVSVTARD-DVPFFGPN- 338
+P + HF A I ++D + + F
Sbjct: 1668 ---NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKG 1724
Query: 339 ------FPQPAIFRADSDFKEFLLTKLINAENAAYKAHKFAKLELRTRSSLLHSLCEELK 392
F QPA+ L E AA+ E+LK
Sbjct: 1725 LLSATQFTQPALT----------LM-----EKAAF---------------------EDLK 1748
Query: 393 EKTREFLGGEGEDTRHGDTSNGS---GTGTRFIDTEHSNFVGVDNE------LGPVL-LS 442
K G + G HS +G E L V+ +
Sbjct: 1749 SK--------------GLIPADATFAG---------HS--LG---EYAALASLADVMSIE 1780
Query: 443 TKTELVGNQSHTRLLLRLKTG-TVHELLPPNCANASPQTMARL---RTRSSL----LHSL 494
+ E+V R G T+ +P + S M + R +S L +
Sbjct: 1781 SLVEVV----FYR-------GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYV 1829
Query: 495 CEELKEKTREFL 506
E + ++T +
Sbjct: 1830 VERVGKRTGWLV 1841
Score = 30.0 bits (67), Expect = 2.7
Identities = 36/226 (15%), Positives = 66/226 (29%), Gaps = 82/226 (36%)
Query: 197 EEELFANKHTSPAFDQFLNLLGQRILLKDHKGYRGGLDTQFRQTGEQAVYQVFKEREI-- 254
+ L A + T PA + L E+A ++ K + +
Sbjct: 1723 KGLLSATQFTQPA-----------LTLM-----------------EKAAFEDLKSKGLIP 1754
Query: 255 ---MF--H----------VSTLLPFTENDPQQLQRKRHIGNDIVAIVFQETNTPFSPDMI 299
F H ++ ++ ++ R G + V ++ + MI
Sbjct: 1755 ADATFAGHSLGEYAALASLADVMSIE--SLVEVVFYR--GMTMQVAVPRDELGRSNYGMI 1810
Query: 300 A------SHFLHAFIVVQVIDPNTPNTRYKVSVTARDDVPFFGPNFP--QPAI---FRAD 348
A + + V++ T + V + V + N Q RA
Sbjct: 1811 AINPGRVAASFSQEALQYVVERVGKRTGWLVEI-----VNY---NVENQQYVAAGDLRA- 1861
Query: 349 SDFKEFLLTKLINAENAAYKAHKFAKLELRTRSSLLHSLCEELKEK 394
L + N N K K +EL+ SL EE++
Sbjct: 1862 -------LDTVTNVLNFI-KLQKIDIIELQKSLSL-----EEVEGH 1894
>3jqo_B TRAO protein; helical outer membrane TM, outer membrane protein
complex, plasmid, transport protein; HET: LDA; 2.60A
{Escherichia coli} PDB: 2ofq_A
Length = 135
Score = 30.3 bits (68), Expect = 0.67
Identities = 15/84 (17%), Positives = 25/84 (29%), Gaps = 16/84 (19%)
Query: 311 QVIDPNTPNTRYKVSVTAR----------DDVPF----FGPNFPQPAIFRADSDFKEFLL 356
Q N +Y +S D+ F F N P ++ + KE L
Sbjct: 14 QTAFAGAKNYQYVMSEQPEMRSIQPVHVWDNYRFTRFEFPANAELPQVYMISASGKETLP 73
Query: 357 TKLINAENAAY-KAHK-FAKLELR 378
+ EN + + +R
Sbjct: 74 NSHVVGENRNIIEVETVAKEWRIR 97
>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 = 30.4 bits (68), Expect = 1.0
Identities = 11/47 (23%), Positives = 15/47 (31%), Gaps = 9/47 (19%)
Query: 388 CEELKEKTREFLGGEGEDTRHGDT---SNGSGTGTRFIDT--EHSNF 429
C E K + + E GD G + +DT E F
Sbjct: 24 CPECKVYPPKIV----ERFSEGDVVCALCGLVLSDKLVDTRSEWRTF 66
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing,
hydrolase, endonu nuclease; 2.85A {Escherichia coli}
PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A
Length = 517
Score = 29.5 bits (67), Expect = 3.0
Identities = 6/17 (35%), Positives = 7/17 (41%)
Query: 481 MARLRTRSSLLHSLCEE 497
M+R R SL S
Sbjct: 394 MSRQRLSPSLGESSHHV 410
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
0.317 0.133 0.391
Gapped
Lambda K H
0.267 0.0541 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,849,632
Number of extensions: 468185
Number of successful extensions: 1114
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1103
Number of HSP's successfully gapped: 19
Length of query: 533
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 435
Effective length of database: 3,965,535
Effective search space: 1725007725
Effective search space used: 1725007725
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: 60 (27.3 bits)