RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 014582
(422 letters)
>1zbt_A RF-1, peptide chain release factor 1; peptide chain release factor
1 (RF-1), structural joint center for structural
genomics, JCSG; 2.34A {Streptococcus mutans}
Length = 371
Score = 478 bits (1234), Expect = e-169
Identities = 136/370 (36%), Positives = 226/370 (61%), Gaps = 4/370 (1%)
Query: 53 STEMLSNDLIK-IMEQRVLAIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHL 109
++ + + + ++ A+E R L L++ P+ + + + ++E R+++ +
Sbjct: 2 GSDKIHHHHHHMNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAV 61
Query: 110 ISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDAD 169
E + + I + +I + S D ++ +MA EEL + ++ + L LLPKD D
Sbjct: 62 YREYKQVVQNIADAQEMIKDASGDPELEEMAKEELKNSKVAKEEYEEKLRFLLLPKDPND 121
Query: 170 ERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAIS 229
+++ ILE+R GG+EA+LFA D+ MY++Y++ +GWKFEV+ + + + G KE A +S
Sbjct: 122 DKNIILEIRGAAGGDEAALFAGDLLNMYQKYAENQGWKFEVMEASANGVGGLKEVVAMVS 181
Query: 230 GVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYR 289
G VY KLK+ESG HRVQRVP+TE GRVHTS +V ++P+ +EV+ + +DLR+D Y
Sbjct: 182 GQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEYEIDPKDLRVDIYH 241
Query: 290 SGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHL 349
+ G+GGQ+ N +AVR+ H+PT + + +Q+ER+Q N+ KA+K++ A++ +
Sbjct: 242 ASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQD 301
Query: 350 SRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQ 409
+ R +G+GDRSERIRTYNFPQ RVTDHR+G+T + ++ G+ LD IDAL+L
Sbjct: 302 EQDAERKSTVGTGDRSERIRTYNFPQNRVTDHRIGLTLQKLDSILSGK-LDEVIDALILY 360
Query: 410 QEMDAIASFG 419
+ +
Sbjct: 361 DQTQKLEELN 370
>3d5a_X RF1, peptide chain release factor 1; ribosome, ribonucleoprotein,
ribosomal protein, RNA-binding, binding, metal-binding,
zinc-finger; 3.21A {Thermus thermophilus} PDB: 2b64_Y
3d5c_X 3mr8_V 3ms0_V
Length = 354
Score = 470 bits (1211), Expect = e-166
Identities = 149/357 (41%), Positives = 225/357 (63%), Gaps = 7/357 (1%)
Query: 65 MEQRVLAIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHLISELRTKQKEIDG 122
M ++ +E LE L++ PE Y ++ ++ + + LI E R ++++
Sbjct: 1 MLDKLDRLEEEYRELEALLSDPEVLKDKGRYQSLSRRYAEMGEVIGLIREYRKVLEDLEQ 60
Query: 123 LKSLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTG 182
+SL+ +D ++ +MA E + ++ L+ L + LLPKD DERD I+E+RAGTG
Sbjct: 61 AESLL----DDPELKEMAKAEREALLARKEALEKELERHLLPKDPMDERDAIVEIRAGTG 116
Query: 183 GEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESG 242
GEEA+LFA D+F MY R++++ G++ EV+ +DL G+ + + G G YG K+ESG
Sbjct: 117 GEEAALFARDLFNMYLRFAEEMGFETEVLDSHPTDLGGFSKVVFEVRGPGAYGTFKYESG 176
Query: 243 IHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTTN 302
+HRVQRVP+TE GR+HTS +VA+LP+A+E D L +++RID R+ G GGQ NTT+
Sbjct: 177 VHRVQRVPVTETQGRIHTSTATVAVLPKAEEEDFALNMDEIRIDVMRASGPGGQGVNTTD 236
Query: 303 SAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQIGSG 362
SAVRV H+PTG+ ++ QD RSQ N+ KAL +L ++L EM+R+ K R QIG+G
Sbjct: 237 SAVRVVHLPTGIMVTCQDSRSQIKNREKALMILRSRLLEMKRAEEAERLRKTRLAQIGTG 296
Query: 363 DRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQEMDAIASFG 419
+RSE+IRTYNFPQ RVTDHR+G T H + ++ G L ++AL + +A+
Sbjct: 297 ERSEKIRTYNFPQSRVTDHRIGFTTHDLEGVLSGH-LTPILEALKRADQERQLAALA 352
>2b3t_B RF-1, peptide chain release factor 1; translation termination,
methylation, conformational changes; HET: SAH; 3.10A
{Escherichia coli} SCOP: e.38.1.1
Length = 360
Score = 470 bits (1211), Expect = e-166
Identities = 157/360 (43%), Positives = 242/360 (67%), Gaps = 8/360 (2%)
Query: 63 KIMEQRVLAIERRSACLENLVNQPE--ASPAEYSKANKELRKLRDSMHLISELRTKQKEI 120
+ ++ A+ R ++ L+ + A + ++E +L D ++ + Q++I
Sbjct: 3 PSIVAKLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQEDI 62
Query: 121 DGLKSLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAG 180
+ + ++ +D +M +MA +EL A ++ ++L+ L LLPKD DER+ LEVRAG
Sbjct: 63 ETAQMML----DDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAG 118
Query: 181 TGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFE 240
TGG+EA+LFA D+F+MY RY++ + W+ E++ +E + GYKE A ISG GVYG+LKFE
Sbjct: 119 TGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFE 178
Query: 241 SGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVR-LRNEDLRIDTYRSGGSGGQHAN 299
SG HRVQRVP TE GR+HTSA +VA++P+ + ++ + DLRIDT+RS G+GGQH N
Sbjct: 179 SGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVN 238
Query: 300 TTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQI 359
TT+SA+R+TH+PTG+ + QDERSQH NKAKAL VL A+++ E ++ + + R +
Sbjct: 239 TTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLL 298
Query: 360 GSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQEMDAIASFG 419
GSGDRS+R RTYNFPQGRVTDHR+ +T + + ++MEG+ LD+ I+ ++ + + D +A+
Sbjct: 299 GSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGK-LDMLIEPIIQEHQADQLAALS 357
>1rq0_A RF-1, peptide chain release factor 1; X-RAY, crystal, peptide
release factor 1, ribosome, structural genomics, BSGC
structure funded by NIH; 2.65A {Thermotoga maritima}
SCOP: e.38.1.1 PDB: 2fvo_A
Length = 342
Score = 454 bits (1171), Expect = e-160
Identities = 138/348 (39%), Positives = 220/348 (63%), Gaps = 15/348 (4%)
Query: 72 IERRSACLENLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECS 131
++ + +E L+ +P+ +P + E K+ + ++ + ++ Q+ I+ L+ E
Sbjct: 1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLR----EEG 56
Query: 132 EDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTGGEEASLFAV 191
E++ ++ +EL ++ Q LL I+E+R GTGGEEA+LFA
Sbjct: 57 ENELEIEKYEKEL------DQLYQELLF----LLSPEASDKAIVEIRPGTGGEEAALFAR 106
Query: 192 DVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRVPL 251
D+F+MY RY+++KGW EV + E+DL G +E + G YG LK+ESG+HRVQRVP+
Sbjct: 107 DLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPV 166
Query: 252 TEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIP 311
TE GR+HTS +VA+LP+ +E D+ +R EDL+I+T+R+ G GGQ+ N T SAVR+TH+P
Sbjct: 167 TESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLP 226
Query: 312 TGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQIGSGDRSERIRTY 371
TG+ +S Q+ERSQ+ NK AL++L A+LY++++ + S+ R QIG+G+RSE+IRTY
Sbjct: 227 TGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTY 286
Query: 372 NFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQEMDAIASFG 419
NFPQ RVTDHR+ T + + ++++G+ LD I L+ + +
Sbjct: 287 NFPQNRVTDHRINYTSYRLQEILDGD-LDEIISKLIEHDIENNLEEVL 333
>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation;
2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X
2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
Length = 365
Score = 263 bits (675), Expect = 3e-85
Identities = 111/310 (35%), Positives = 171/310 (55%), Gaps = 13/310 (4%)
Query: 109 LISELRTKQKEIDGLKSLIYECSEDKDMLDMATEELCLAIDEE-----KRLQSLLLKSLL 163
+ E ++ +D +SL + ++++ E A+ E K+L L ++LL
Sbjct: 48 VSQEAARLRRTVDTFRSLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLL 107
Query: 164 PKDDADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKE 223
E++ IL ++ G GG EA +A + +MY R+++++G++ EVV +T G
Sbjct: 108 -NFPHAEKNAILTIQPGAGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDY 166
Query: 224 ASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADE-VDVRLRNED 282
A + G YG L E+G+HR+ R + SGR HTS V ++P+ DE V+V L+ E+
Sbjct: 167 AQILVKGENAYGLLSPEAGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEE 226
Query: 283 LRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEM 342
LRID R+ G GGQ NTT+SAVRV H+PTG+T++ Q RSQ NK ALK+L A+LYE+
Sbjct: 227 LRIDVMRASGPGGQGVNTTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYEL 286
Query: 343 ERSRIHLSRSKLRSEQ--IGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLD 400
ER + LR E I G +IR+Y + V DHR G+ H ++++G+ L
Sbjct: 287 ERKKREEELKALRGEVRPIEWGS---QIRSYVLDKNYVKDHRTGLMRHDPENVLDGD-LM 342
Query: 401 IFIDALLLQQ 410
I A L +
Sbjct: 343 DLIWAGLEWK 352
>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
mimicry, translation; 1.81A {Escherichia coli} SCOP:
e.38.1.1 PDB: 1mi6_A 1ml5_Z*
Length = 365
Score = 261 bits (668), Expect = 3e-84
Identities = 115/345 (33%), Positives = 189/345 (54%), Gaps = 14/345 (4%)
Query: 71 AIERRSACLENLVNQPEA--SPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIY 128
A + R + + QP+ P KE L + + +++ +++ GL L
Sbjct: 29 AKKERLEEVNAELEQPDVWNEPERAQALGKERSSLEAVVDTLDQMKQGLEDVSGLLELAV 88
Query: 129 ECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDDADERDCILEVRAGTGGEEASL 188
E ++D++ + A EL E++L L + + + D DC L+++AG+GG EA
Sbjct: 89 E-ADDEETFNEAVAEL---DALEEKLAQLEFRRMF-SGEYDSADCYLDIQAGSGGTEAQD 143
Query: 189 FAVDVFKMYERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRVQR 248
+A + +MY R+++ +G+K E++ +E ++ G K + ISG YG L+ E+G+HR+ R
Sbjct: 144 WASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVR 203
Query: 249 VPLTEKSGRVHTSAVSVAILPQADE-VDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRV 307
+ GR HTS S + P+ D+ +D+ + DLRID YR+ G+GGQH N T SAVR+
Sbjct: 204 KSPFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRI 263
Query: 308 THIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSEQ--IGSGDRS 365
THIPTG+ Q++RSQH NK +A+K + AKLYE+E + + + + + IG G
Sbjct: 264 THIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYEVEMQKKNAEKQAMEDNKSDIGWGS-- 321
Query: 366 ERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDALLLQQ 410
+IR+Y R+ D R G+ +++G LD FI+A L
Sbjct: 322 -QIRSYVLDDSRIKDLRTGVETRNTQAVLDGS-LDQFIEASLKAG 364
>2rsm_A Probable peptide chain release factor C12ORF65 HO mitochondrial;
GGQ domain, translation; NMR {Mus musculus}
Length = 115
Score = 164 bits (416), Expect = 5e-50
Identities = 30/122 (24%), Positives = 49/122 (40%), Gaps = 12/122 (9%)
Query: 226 AAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVD-VRLRNEDLR 284
+ G +G R+Q P G +A +V + + D + L +L
Sbjct: 1 GSSGSSGKWG--------LRLQEKPALLFPG---MAASTVQVAGRKDYPALLPLNESELE 49
Query: 285 IDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMER 344
+ G GGQ N T++ V + H+P+G+ + RS N+ A KVL K+
Sbjct: 50 EQFVKGHGPGGQATNKTSNCVVLKHVPSGIVVKCHQTRSVDQNRKIARKVLQEKVDVFYN 109
Query: 345 SR 346
S
Sbjct: 110 SG 111
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue F
alternative rescue factor, ARFB, release factor, rescue
of ribosomes; 3.20A {Escherichia coli} PDB: 2jy9_A
Length = 140
Score = 65.9 bits (161), Expect = 2e-13
Identities = 23/97 (23%), Positives = 38/97 (39%), Gaps = 24/97 (24%)
Query: 272 DEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVT----------------------- 308
V + + +L I R+ G+GGQH N T++A+ +
Sbjct: 4 ISRHVAIPDGELEITAIRAQGAGGQHVNKTSTAIHLRFDIRASSLPEYYKERLLAASHHL 63
Query: 309 -HIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMER 344
+ I Q+ RSQ +N+ AL L A + E+
Sbjct: 64 ISSDGVIVIKAQEYRSQELNREAALARLVAMIKELTT 100
>2jva_A Peptidyl-tRNA hydrolase domain protein; GFT hydrolase, structural
genomics, PSI-2, protein STRU initiative; NMR
{Pseudomonas syringae PV}
Length = 108
Score = 63.8 bits (155), Expect = 8e-13
Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 24/94 (25%)
Query: 275 DVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTG--------------------- 313
+V L + ++ + R+ G+GGQ+ N +SA+ +
Sbjct: 7 NVHLPDAEIELTAIRAQGAGGQNVNKVSSAMHLRFDINASSLPPFYKERLLALNDSRITS 66
Query: 314 ---MTISIQDERSQHMNKAKALKVLCAKLYEMER 344
+ + Q R+Q N+A AL L + +
Sbjct: 67 DGVIVLKAQQYRTQEQNRADALLRLSELIVNAAK 100
>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 = 64.9 bits (157), Expect = 2e-11
Identities = 62/449 (13%), Positives = 123/449 (27%), Gaps = 109/449 (24%)
Query: 35 WFVQRAAA---TPSLSNFRSYSTEM--LSND---LIKIMEQRVLAIERRSACLENLVNQP 86
+ + PS+ R Y + L ND K R+ + L L +P
Sbjct: 93 FLMSPIKTEQRQPSM-MTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL--RP 149
Query: 87 EAS--------------PAEYSKANKELRKLRDSMHLIS--ELRTKQKEIDGLKSLIYEC 130
+ + + K K+ + ++ + + ++ L+ L+Y+
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 131 SEDKDMLDMATEELCLAIDEEK-RLQSLLL-----KSLLPKDD-ADER-------DC-IL 175
+ + + L I + L+ LL LL + + + C IL
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269
Query: 176 EVRAGTGGEEASLFAVDVFKMYERYSQKKGWKFE----------VVGVTESDLRGYKEAS 225
+ T + + + DL +E
Sbjct: 270 -L---TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP--REVL 323
Query: 226 A----AISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVDVRLRNE 281
+S + G+ S+ +L + + R +
Sbjct: 324 TTNPRRLSIIA----ESIRDGLATWDNWKHVNCDKLTTIIESSLNVL---EPAEYRKMFD 376
Query: 282 DLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISI---QDERSQHMNKAKAL--KVLC 336
L + + HIPT + +S+ +S M L L
Sbjct: 377 RLSV--FPPS----------------AHIPT-ILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 337 AKLYEMERSRIHLSRSKLRSEQIGSGDRSERIRT-YNFPQGRVTDHRVG----------I 385
K + I +L+ + I YN P+ +D + I
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI 477
Query: 386 THHAISDMMEGENLDIFIDALL----LQQ 410
HH + ++ E + +F L L+Q
Sbjct: 478 GHH-LKNIEHPERMTLFRMVFLDFRFLEQ 505
Score = 49.5 bits (117), Expect = 2e-06
Identities = 32/209 (15%), Positives = 57/209 (27%), Gaps = 77/209 (36%)
Query: 28 NPLL-----------HQRWFVQRAAATPSLSNFRSYSTEMLSNDLIKIMEQRVLAIERRS 76
NP W N++ + + L+ I+E
Sbjct: 326 NPRRLSIIAESIRDGLATW-----------DNWKHVNCDKLT----TIIE---------- 360
Query: 77 ACLENLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLKSLIYECSEDKDM 136
+ L L PAEY K L S H+ + L L + ++ +
Sbjct: 361 SSLNVL------EPAEYRKMFDRLSVFPPSAHIPTIL---------LSLIWFDVIKS--- 402
Query: 137 LDMATEELCLAIDEEKRLQSLLLKSLLPKDDADER----DCILEVRAGTGGEEASLFAVD 192
D + L SL+ K + LE++ E +L
Sbjct: 403 ------------DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKV-KLENEYALHR-- 447
Query: 193 VFKMYERYSQKKGWKFEVVGVTESDLRGY 221
+ + Y+ K + + + D Y
Sbjct: 448 --SIVDHYNIPKTFDSDDLIPPYLD--QY 472
Score = 46.4 bits (109), Expect = 1e-05
Identities = 50/300 (16%), Positives = 104/300 (34%), Gaps = 96/300 (32%)
Query: 5 NWAIALHLGALRQLES-SSSISHRNPLLHQRWFVQRAAATPSLSNFRSYSTEMLSNDLIK 63
NW H+ + SS++ P +++ F + LS F
Sbjct: 346 NW---KHVNCDKLTTIIESSLNVLEPAEYRKMFDR-------LSVFP---------PSAH 386
Query: 64 IMEQRVLAI---ERRSACLENLVNQPEASPAEYSKANKELRKLRDSMHLIS-ELRTKQKE 119
I +L++ + + + +VN+ +YS K+ ++ S+ I EL+ K +
Sbjct: 387 IPTI-LLSLIWFDVIKSDVMVVVNKLH----KYSLVEKQPKESTISIPSIYLELKVKLEN 441
Query: 120 IDGL-KSLI--YE-----CSED--KDMLD----------MATEELCLAIDEEKRLQSLLL 159
L +S++ Y S+D LD + E + + + L
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEH---PERMTLFRMVFL 498
Query: 160 KSLLPKDDADERDCILE--VRAGTGGEEASLFAVDV---FKMYERYSQKKGWKFEVVGVT 214
D R LE +R + AS ++ K Y+ Y +
Sbjct: 499 ---------DFR--FLEQKIRHDSTAWNASGSILNTLQQLKFYKPY------------IC 535
Query: 215 ESDLRGYKEASAAISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEV 274
++D + Y+ AI L F + +++ + K +T + +A++ + + +
Sbjct: 536 DNDPK-YERLVNAI--------LDF---LPKIEENLICSK----YTDLLRIALMAEDEAI 579
Score = 40.2 bits (93), Expect = 0.001
Identities = 61/431 (14%), Positives = 120/431 (27%), Gaps = 139/431 (32%)
Query: 59 NDLIKIMEQR---------VLAIERR---SACLENLVNQPEASPAEYSKANKELRKLRDS 106
D++ + E V + + +++++ + LR
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSK----------DAVSGTLR-- 66
Query: 107 MHLISELRTKQKEI------DGLK--------SLIYECSEDKDMLDMATEELCLAIDEEK 152
L L +KQ+E+ + L+ + E + M M I++
Sbjct: 67 --LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM-------YIEQRD 117
Query: 153 RLQSLLLKSLLPKDDADERDCILEVRA--------------GTGGEEASLFAVDVFKMYE 198
RL + + K + L++R G G + A+DV Y+
Sbjct: 118 RLYN--DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 199 RYSQKKG---W-KFEVVGVTESDLRGYKEASAAISGVGVYG-------KLKFESGIHRVQ 247
+ W + E+ L ++ I KL+ S ++
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELR 235
Query: 248 RVPLTEKSGRVHTSAVSVAILPQADEV-DVRLRNE-DLR---IDTYRSGGSGGQHANTTN 302
R+ L K + +L V + + N +L + T R T+
Sbjct: 236 RL-LKSKPYE-----NCLLVL---LNVQNAKAWNAFNLSCKILLTTRF-------KQVTD 279
Query: 303 --SAVRVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRIHLSRSKLRSE--- 357
SA THI D S + + L K + L E
Sbjct: 280 FLSAATTTHIS-------LDHHSMTLTPDEVKS-LLLKY-------LDCRPQDLPREVLT 324
Query: 358 -------QIGSGDRSERIRTYNFPQGRVTDHRVGITHHAISDMMEGENLDIFIDAL---L 407
I R N+ + ++ ++E ++ L
Sbjct: 325 TNPRRLSIIAESIRDGLATWDNWKH---------VNCDKLTTIIE-----SSLNVLEPAE 370
Query: 408 LQQEMDAIASF 418
++ D ++ F
Sbjct: 371 YRKMFDRLSVF 381
>1j26_A Immature colon carcinoma transcript 1; peptide chain release
factors, RF-1, the GGQ motif, immature carcinoma
transcript 1; NMR {Mus musculus} SCOP: d.50.4.1
Length = 112
Score = 58.6 bits (141), Expect = 5e-11
Identities = 19/98 (19%), Positives = 31/98 (31%), Gaps = 25/98 (25%)
Query: 269 PQADEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTG--------------- 313
A + + + L I RS G GGQ+ N NS V
Sbjct: 8 EHAKQASSYIPLDRLSISYCRSSGPGGQNVNKVNSKAEVRFHLASADWIEEPVRQKIALT 67
Query: 314 ----------MTISIQDERSQHMNKAKALKVLCAKLYE 341
+ ++ + R Q N A+ L+ + + E
Sbjct: 68 HKNKINKAGELVLTSESSRYQFRNLAECLQKIRDMIAE 105
>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 = 52.0 bits (124), Expect = 3e-07
Identities = 54/297 (18%), Positives = 84/297 (28%), Gaps = 122/297 (41%)
Query: 98 KELRKLRDSM--HLISELRTKQKEIDG-----LKSLIYECSEDKDMLD---------MAT 141
K +R+ +M I + + K ++I S + +K +L
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFR--SEKGLLSATQFTQPALTLM 1739
Query: 142 EELCLAIDEEKRLQSLLLKS--LLPKDDADERDCILEVRAG---TGGEEASLFAVDVFKM 196
E A E LKS L+P D AG GE
Sbjct: 1740 E---KAAFE-------DLKSKGLIPADA---------TFAGHSL--GE------------ 1766
Query: 197 YERYSQKKGWKFEVVGVTESDLRGYKEASAAISGVGVYGKLKFESGIHRV-QR------- 248
Y+ A A+++ V + ES + V R
Sbjct: 1767 ---YA----------------------ALASLADV-----MSIESLVEVVFYRGMTMQVA 1796
Query: 249 VPLTEKSGRVHTSAVSVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQH---ANTTNSAV 305
VP E GR + + AI P V E L+ R G G N N
Sbjct: 1797 VPRDE-LGRSNYGMI--AINP--GRVAASFSQEALQYVVERVGKRTGWLVEIVNY-NVE- 1849
Query: 306 RVTHIPTGMTISIQDERSQHMNKAKALKVLCAKLYEMERSRI---HLSRSKLRSEQI 359
+ + +AL + L ++ +I L +S L E++
Sbjct: 1850 -------NQQYVA----AGDL---RALDTVTNVLNFIKLQKIDIIELQKS-LSLEEV 1891
Score = 41.6 bits (97), Expect = 5e-04
Identities = 68/429 (15%), Positives = 131/429 (30%), Gaps = 163/429 (37%)
Query: 12 LGALRQLESSSSISHRNPLLHQRWFVQRAAATPSLSNF-RSYSTEMLSND-------LIK 63
LG + L S + + +L+ L+ F Y + ND L++
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNL-----------CLTEFENCY---LEGNDIHALAAKLLQ 110
Query: 64 IMEQRVLAIER--RS---ACLENLVNQPEASPAE---YSKANKELRKLRDSMHLI----- 110
+ ++ + ++ A + +P + + + +L I
Sbjct: 111 ENDTTLVKTKELIKNYITAR--IMAKRPFDKKSNSALFRAVGEGNAQL----VAIFGGQG 164
Query: 111 ------SELRTKQKEIDGLKSLIYECSED--KDMLDMATEELCLAIDEEKRLQSLLLKSL 162
ELR +Y+ D++ + E L I + + + L
Sbjct: 165 NTDDYFEELRD-----------LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL 213
Query: 163 LPKDDADERDCI--LEVRAGTGGEE--AS------LFAVDVFKMYERYSQKKGWKFEVVG 212
+ + LE + T ++ S L V Y ++ ++G
Sbjct: 214 ---------NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAK-------LLG 257
Query: 213 VTESDLRGYKE----------ASAAISGVG--------VYGKLK--FESGIHRVQRVPLT 252
T +LR Y + + AI+ V + F G+ + P
Sbjct: 258 FTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYP-- 315
Query: 253 EKSGRVHTSAVSVAILPQADEVD---------VR-LRNEDLRIDTYRSGGSGGQHANTTN 302
+++ +IL + E + + L E ++ + N TN
Sbjct: 316 -------NTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ-----------DYVNKTN 357
Query: 303 SAVRVTHIPTGMTISIQDERSQHMNKAKALKVLC---AKLY-------------EMERSR 346
+H+P G + I S N AK L V+ LY +++SR
Sbjct: 358 -----SHLPAGKQVEI----SLV-NGAKNL-VVSGPPQSLYGLNLTLRKAKAPSGLDQSR 406
Query: 347 IHLSRSKLR 355
I S KL+
Sbjct: 407 IPFSERKLK 415
Score = 41.6 bits (97), Expect = 5e-04
Identities = 69/438 (15%), Positives = 125/438 (28%), Gaps = 169/438 (38%)
Query: 14 ALRQLESSSSISHRNPLLHQRWFVQRAAATPSLS---------NFRSYSTEM-------- 56
A + + L RA + N Y E+
Sbjct: 129 ARIMAKRPFDKKSNSALF-------RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYH 181
Query: 57 -LSNDLIKIMEQRVLAIERRSACLENLVNQPEASPAEYSKANKELRKLRDSMHLISELRT 115
L DLIK + L L+ + +++ ++++ L
Sbjct: 182 VLVGDLIKFS----------AETLSELIRTTLDAEKVFTQ----------GLNILEWLEN 221
Query: 116 KQK--EIDGLKS------LIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSLLPKDD 167
+ D L S LI ++ +A ++ LL
Sbjct: 222 PSNTPDKDYLLSIPISCPLIG-------VIQLA--------------HYVVTAKLLGFTP 260
Query: 168 ADERDCILEVRAGTGGEEASLFAVDVFKMYERYSQKKGWK-FEVVGVTESDLRGYKEASA 226
+ R + + TG + + AV + ++ W+ F +
Sbjct: 261 GELRSYL---KGATGHSQGLVTAVAI-------AETDSWESF------------FVSVRK 298
Query: 227 AISGVGVYGKLKFESGIHRVQRVPLTEKSGRVHTSAVSVAILPQADEVD---------VR 277
AI + F G+ + P +++ +IL + E + +
Sbjct: 299 AI-------TVLFFIGVRCYEAYP---------NTSLPPSILEDSLENNEGVPSPMLSIS 342
Query: 278 -LRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERSQHMNKAKALKVLC 336
L E ++ + N TN +H+P G + I S N AK L V+
Sbjct: 343 NLTQEQVQ-----------DYVNKTN-----SHLPAGKQVEI----SLV-NGAKNL-VVS 380
Query: 337 ---AKLYEMERSRIHLSRSKLRSEQIGSGDRSERIRTYNFPQGR--VTDHRVG-IT---H 387
LY L+ + LR + SG RI F + R +R + H
Sbjct: 381 GPPQSLY-------GLNLT-LRKAKAPSGLDQSRIP---FSE-RKLKFSNRFLPVASPFH 428
Query: 388 HAISDMMEGENLDIFIDA 405
S ++ + I D
Sbjct: 429 ---SHLLVPASDLINKDL 443
Score = 39.3 bits (91), Expect = 0.003
Identities = 30/191 (15%), Positives = 65/191 (34%), Gaps = 48/191 (25%)
Query: 19 ESSSSISHRNP--LLHQRWFVQRAAATPSLSNFR-----------------S---YS--- 53
E S+S + R+ LL F Q A + F S Y+
Sbjct: 1712 EHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALA 1771
Query: 54 --TEMLS-NDLIKIMEQRVLAIERRSACLENLVNQPEASPAEYS---------KANKELR 101
+++S L++++ R + + + V + E + Y A+
Sbjct: 1772 SLADVMSIESLVEVVFYRGMTM-------QVAVPRDELGRSNYGMIAINPGRVAASFSQE 1824
Query: 102 KLRDSMHLISELRTKQKEI--DGLKSLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLL 159
L+ + + + EI +++ Y + D LD T L + +++ + L
Sbjct: 1825 ALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTN--VLNFIKLQKIDIIEL 1882
Query: 160 KSLLPKDDADE 170
+ L ++ +
Sbjct: 1883 QKSLSLEEVEG 1893
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 33.5 bits (77), Expect = 0.14
Identities = 21/120 (17%), Positives = 43/120 (35%), Gaps = 3/120 (2%)
Query: 27 RNPLLHQRWFVQRAAATPSLSNFRSYSTEMLSNDLIKIMEQRVLAIERRSACLENLVNQP 86
R L + A +R + L KI + V ++ LEN + Q
Sbjct: 875 RGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKL-KIEARSVERYKKLHIGLENKIMQL 933
Query: 87 EASPAEYSKANKELRKLRDSM--HLISELRTKQKEIDGLKSLIYECSEDKDMLDMATEEL 144
+ E +K K L + +++ +E + +++ L+ E + + EE+
Sbjct: 934 QRKIDEQNKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQEEI 993
>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 = 31.5 bits (70), Expect = 0.27
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 12/36 (33%)
Query: 198 ERYSQKKGWKFEVVGVTESDLRGYKEASA---AISG 230
E+ + KK ++ L+ Y + SA AI
Sbjct: 18 EKQALKK---------LQASLKLYADDSAPALAIKA 44
Score = 31.1 bits (69), Expect = 0.39
Identities = 8/36 (22%), Positives = 18/36 (50%), Gaps = 8/36 (22%)
Query: 66 EQRVLAIERRSACLENLVN--QPEASPAEYSKANKE 99
E++ A+++ L+ + +++PA KA E
Sbjct: 18 EKQ--ALKK----LQASLKLYADDSAPALAIKATME 47
>2ygl_A Blood group A-and B-cleaving endo-beta-galactosid; hydrolase,
carbohydrate-binding module, blood group antigen; 2.10A
{Streptococcus pneumoniae} PDB: 2ygm_A*
Length = 354
Score = 29.9 bits (66), Expect = 1.8
Identities = 21/190 (11%), Positives = 62/190 (32%), Gaps = 25/190 (13%)
Query: 207 KFE-VVGVTESDLRGYKEASAAISGVGVY--GKLKFESGIHRVQRVPLTEKSGRVHTSAV 263
KFE +G+ + + A + + + GK+ + S + + R +T A
Sbjct: 82 KFETYIGI-DQSANSSRSDHAVVDRIEIEIDGKVVYSSSV-------TNPEGFRYNTQAQ 133
Query: 264 SVAILPQADEVDVRLRNEDLRIDTYRSGGSGGQHANTTNSAVRVTHIPTGMTISIQDERS 323
+ V + + + + ++ + G ++ + T +T + ++
Sbjct: 134 FI-------SVTIPQNAKKISLKSFAGEHTWGDEVVFADAKLIKTVSTQTITPDLLNKGI 186
Query: 324 QHMNKAKALKVLCAK-LYEMERSRIHLSRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHR 382
L+ + A + + + + +G + +I+ + +
Sbjct: 187 NGGVYLSDLEWVDATHGDDDKSKTVQKDKP---FTPGNNGS-NNKIKLLIDGKEVEFNK- 241
Query: 383 VGITHHAISD 392
G+ A +
Sbjct: 242 -GLGTVASNP 250
>1o73_A Tryparedoxin; electron transport, trypanosomatid, thioredoxin;
2.28A {Trypanosoma brucei brucei} SCOP: c.47.1.10
Length = 144
Score = 28.0 bits (63), Expect = 3.3
Identities = 7/19 (36%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 195 KMYERYSQKKGWKFEVVGV 213
+ YE++ K FEVV +
Sbjct: 52 EFYEKHHVAKN--FEVVLI 68
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment
2, heavy meromyosin, essential light chain, motor
protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1
PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 28.6 bits (64), Expect = 5.0
Identities = 13/101 (12%), Positives = 34/101 (33%), Gaps = 2/101 (1%)
Query: 62 IKIMEQRVLAIERRSACLENLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEID 121
++ E ++ + + + E N +L K R L + +
Sbjct: 964 LEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNKLTKERK--LLEERVSDLTTNLA 1021
Query: 122 GLKSLIYECSEDKDMLDMATEELCLAIDEEKRLQSLLLKSL 162
+ ++ K+ + EL + + +E++ + L K
Sbjct: 1022 EEEEKAKNLTKLKNKHESMISELEVRLKKEEKSRQELEKIK 1062
>1bf5_A Signal transducer and activator of transcription 1-alpha/beta;
complex (SH2 domain/DNA), SH2 domain, transcription
factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP:
a.47.1.1 b.2.5.5 d.93.1.1
Length = 575
Score = 27.9 bits (61), Expect = 7.1
Identities = 20/124 (16%), Positives = 44/124 (35%), Gaps = 13/124 (10%)
Query: 65 MEQRVLAIERRSACLENLVNQPEASPAEYSKANKELRKLRDSMHLISELRTKQKEIDGLK 124
++ +V ++ + C+E+ + E EY K L+ + +++ KQ++ LK
Sbjct: 7 LDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQ-LLLK 65
Query: 125 SLIYECSED--------KDMLDMATEELCLAIDEE----KRLQSLLLKSLLPKDDADERD 172
+ ++L++ I++E KR Q P D+
Sbjct: 66 KMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQ 125
Query: 173 CILE 176
Sbjct: 126 NWFT 129
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 0.363
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,266,455
Number of extensions: 380305
Number of successful extensions: 804
Number of sequences better than 10.0: 1
Number of HSP's gapped: 777
Number of HSP's successfully gapped: 33
Length of query: 422
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 326
Effective length of database: 4,021,377
Effective search space: 1310968902
Effective search space used: 1310968902
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: 59 (26.7 bits)