RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10034
(399 letters)
>3vbb_A Seryl-tRNA synthetase, cytoplasmic; coiled-coil, ligase; 2.89A
{Homo sapiens}
Length = 522
Score = 479 bits (1236), Expect = e-168
Identities = 251/502 (50%), Positives = 305/502 (60%), Gaps = 111/502 (22%)
Query: 1 MVLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
MVLDLDLFR +KGGDP +R+ Q+ RFK+ LVD++++ D +WR+ R +ADN NK KNLC
Sbjct: 1 MVLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLC 60
Query: 61 SK----------------------------------------------VIGEKMKAKEPV 74
SK +I E + +
Sbjct: 61 SKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAE 120
Query: 75 GDS---------STLPGNHLHPSVPVSNNEDE-NGIVRTKGDTEVRKKYSHVDLITMIDG 124
+ N LHPSVP+SN+ED N + R GD VRKKYSHVDL+ M+DG
Sbjct: 121 RIKLEAERFENLREIG-NLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDG 179
Query: 125 VDSEAGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQ 184
+ E GA+VAG RGYFLKG V L+ L+QYAL +GY P+YTPFFMRKEVMQEVAQ
Sbjct: 180 FEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQ 239
Query: 185 LAQFDEELYKVIGKGEKVGDSAPEKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYL 244
L+QFDEELYKVIGKG + D + D+KYLIATSEQPI A+HRD WL LPI+Y
Sbjct: 240 LSQFDEELYKVIGKGSEKSDD----NSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYA 295
Query: 245 GVSTCFRQE--------------------------------------DLTKS-------- 258
G+STCFRQE ++ +
Sbjct: 296 GLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSL 355
Query: 259 -IAYRVVNIVSGALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKK 317
I Y +VNIVSG+LNHAA+KKLDLEAWFPGSGAFRELVSCSNC DYQ+RRL +RYGQTKK
Sbjct: 356 GIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKK 415
Query: 318 MNEKIEFVHMLNATACATTRVICAILETHQTETGVRIPDCLRKFVPAVYVNEAGEIPFVK 377
M +K+EFVHMLNAT CATTR ICAILE +QTE G+ +P+ L++F+P IPFVK
Sbjct: 416 MMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQE---LIPFVK 472
Query: 378 TAPIDEEETKKQKKQKEGMKKK 399
API++E +KKQKKQ EG KKK
Sbjct: 473 PAPIEQEPSKKQKKQHEGSKKK 494
>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis,
CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA
synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A*
3qo8_A* 3qo5_A
Length = 485
Score = 478 bits (1233), Expect = e-168
Identities = 180/481 (37%), Positives = 235/481 (48%), Gaps = 106/481 (22%)
Query: 2 VLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCS 61
+LD++ F EKGGDPE ++ +QK R +VELVD++I +W + R D NK N
Sbjct: 1 MLDINAFLVEKGGDPEIIKASQKKRGDSVELVDEIIAEYKEWVKLRFDLDEHNKKLNSVQ 60
Query: 62 KVIGEKMKAKEPVGD-----------------------------SSTLPGNHLHPSVPVS 92
K IG++ KAKE D + + N +H SV S
Sbjct: 61 KEIGKRFKAKEDAKDLIAEKEKLSNEKKEIIEKEAEADKNLRSKINQVG-NIVHESVVDS 119
Query: 93 NNEDENGIVRTKGDTEVR------------KKYSHVDLITMIDGVDSEAGAIVAGGRGYF 140
+E+ N +VRT + K SH +++ +DG D E G + G RGYF
Sbjct: 120 QDEENNELVRTWTPENYKKPEQIAAATGAPAKLSHHEVLLRLDGYDPERGVRIVGHRGYF 179
Query: 141 LKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGE 200
L+ V L L+ Y LS KGY PL P M KEVM + AQL+QFDEELYKVI
Sbjct: 180 LRNYGVFLNQALINYGLSFLSSKGYVPLQAPVMMNKEVMAKTAQLSQFDEELYKVIDGE- 238
Query: 201 KVGDSAPEKDELDDKYLIATSEQPICAVHRDSWL--PEASLPIRYLGVSTCFRQE----- 253
D+KYLIATSEQPI A H W P LP+RY G S+CFR+E
Sbjct: 239 ------------DEKYLIATSEQPISAYHAGEWFESPAEQLPVRYAGYSSCFRREAGSHG 286
Query: 254 -------------------------------DLTKS---------IAYRVVNIVSGALNH 273
+ + YRVV IVSG LN+
Sbjct: 287 KDAWGIFRVHAFEKIEQFVLTEPEKSWEEFDRMIGCSEEFYQSLGLPYRVVGIVSGELNN 346
Query: 274 AAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATAC 333
AAAKK DLEAWFP ++ELVSCSNC DYQSR L +R G ++ ++ ++VH LN+T
Sbjct: 347 AAAKKYDLEAWFPFQQEYKELVSCSNCTDYQSRNLEIRCGIKQQNQQEKKYVHCLNSTLS 406
Query: 334 ATTRVICAILETHQTETGVRIPDCLRKFVPAVYVNEAGEIPFVKTAPIDEEETKKQKKQK 393
AT R IC ILE +Q E G+ IP+ LRK++P IP++K P + KK K +
Sbjct: 407 ATERTICCILENYQKEDGLVIPEVLRKYIPGEPE----FIPYIKELPKNTTSVKKAKGKN 462
Query: 394 E 394
Sbjct: 463 P 463
>3lss_A Seryl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase,
AARS, serrs, translation, ATP-binding,
nucleotide-binding, structural genomics; HET: ATP; 1.95A
{Trypanosoma brucei} PDB: 3lsq_A*
Length = 484
Score = 433 bits (1115), Expect = e-150
Identities = 182/500 (36%), Positives = 242/500 (48%), Gaps = 131/500 (26%)
Query: 1 MVLDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
MVLD+ LFR E G +R++Q+ RF + ++VD +IE D KWR+ + + K N+C
Sbjct: 6 MVLDIQLFRDETG--ANIIRESQRRRFADPDIVDAIIEADKKWRRTQFLTEASKKLINIC 63
Query: 61 S-------------------------------------------------KVIGEKMKAK 71
S K + +++
Sbjct: 64 SKAVGAKKKAKEADGDTSEIPPQVKEAYENGTLKGEQVEQLCVLQLKQLSKDLSDQVAGL 123
Query: 72 EPVGDS---------STLPGNHLHPSVPVSNNEDE-NGIVRTKGDTEVRKKYSHVDLITM 121
+ N LH SVP++ +E+ N +VRT G+T R K +HV ++
Sbjct: 124 AKEAQQLEEERDKLMLNVG-NILHESVPIAQDEETGNTVVRTFGNTTKRAKLNHVSIMER 182
Query: 122 IDGVDSE-AGAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQ 180
+ +D+ A +AGGR Y LKG V LQV LV Y+L +++GYTP Y PFF+ ++VM
Sbjct: 183 LGMMDTSKAVTSMAGGRSYVLKGGLVQLQVALVSYSLDFLVKRGYTPFYPPFFLNRDVMG 242
Query: 181 EVAQLAQFDEELYKVIGKGEKVGDSAPEKDELDDKYLIATSEQPICAVHRDSWLPEASLP 240
EVAQL+QFDEELY+V G G D KYLIATSE PI A HR W E P
Sbjct: 243 EVAQLSQFDEELYQVSGDG-------------DKKYLIATSEMPIAAYHRGRWFTELKEP 289
Query: 241 IRYLGVSTCFRQE--------------------------------------DLTKS---- 258
++Y G+STCFR+E D+ +
Sbjct: 290 LKYAGMSTCFRKEAGAHGRDTLGIFRVHQFDKIEQFVVCSPRQEESWRHLEDMITTSEEF 349
Query: 259 -----IAYRVVNIVSGALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYG 313
+ YRVVNI SGALN+AAAKK DLEAWFP SGAFRELVSCSNC DYQS+ + RYG
Sbjct: 350 NKSLGLPYRVVNICSGALNNAAAKKYDLEAWFPASGAFRELVSCSNCTDYQSQSVNCRYG 409
Query: 314 ---QTKKMNEKIEFVHMLNATACATTRVICAILETHQTETGVRIPDCLRKFVPAVYVNEA 370
+ E+ HMLN T CA TR +C I E +QTE GV IPD LR ++ + +
Sbjct: 410 PNLRGTAAQNVKEYCHMLNGTLCAITRTMCCICENYQTEEGVVIPDVLRPYMMGIEM--- 466
Query: 371 GEIPFVKTAPIDEEETKKQK 390
I F A + K +
Sbjct: 467 --IRFENNAQAEGTTPDKGE 484
>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; HET: SSA; 2.60A {Pyrococcus
horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A
Length = 455
Score = 307 bits (788), Expect = e-101
Identities = 145/458 (31%), Positives = 212/458 (46%), Gaps = 121/458 (26%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFK--NVELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
LD+ L R +PE V+ + R + V+ VD++++ D +WR + + +N
Sbjct: 2 LDIKLIRE----NPELVKNDLIKRGELEKVKWVDEILKLDTEWRTKLKEINRLRHERNKI 57
Query: 61 SKVIGEKMKAKEP----------VGDS-------------------STLPGNHLHPSVPV 91
+ IG++ K EP + LP N HPSVPV
Sbjct: 58 AVEIGKRRKKGEPVDELLAKSREIVKRIGELENEVEELKKKIDYYLWRLP-NITHPSVPV 116
Query: 92 SNNEDENGIVRTKGDTEVRKKYS----------------------HVDLITMIDGVDSEA 129
+E++N +R G V K + HVDL+ ++ G D
Sbjct: 117 GKDENDNVPIRFWGKARVWKGHLERFLEQSQGKMEYEILEWKPKLHVDLLEILGGADFAR 176
Query: 130 GAIVAGGRGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFD 189
A V+G R Y+L V L + L+++AL + IEKG+TP+ P+ +R+ V + F+
Sbjct: 177 AAKVSGSRFYYLLNEIVILDLALIRFALDRLIEKGFTPVIPPYMVRRFVEEGSTSFEDFE 236
Query: 190 EELYKVIGKGEKVGDSAPEKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTC 249
+ +YKV E +D YLI T+E P+ +H + L LP+ Y+GVS C
Sbjct: 237 DVIYKV---------------EDEDLYLIPTAEHPLAGMHANEILDGKDLPLLYVGVSPC 281
Query: 250 FRQE------------------------------------DLTKS---------IAYRVV 264
FR+E + ++ I YRVV
Sbjct: 282 FRKEAGTAGKDTKGIFRVHQFHKVEQFVYSRPEESWEWHEKIIRNAEELFQELEIPYRVV 341
Query: 265 NIVSGALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEF 324
NI +G L + AAKK D+EAW PG G FRE+VS SNC D+Q+RRL +R+ + +EK +
Sbjct: 342 NICTGDLGYVAAKKYDIEAWMPGQGKFREVVSASNCTDWQARRLNIRF--RDRTDEKPRY 399
Query: 325 VHMLNATACATTRVICAILETHQTETG-VRIPDCLRKF 361
VH LN+TA AT+R I AILE HQ E G VRIP L K+
Sbjct: 400 VHTLNSTAIATSRAIVAILENHQEEDGTVRIPKVLWKY 437
>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}
Length = 501
Score = 279 bits (715), Expect = 8e-90
Identities = 100/469 (21%), Positives = 176/469 (37%), Gaps = 114/469 (24%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNV--ELVDKVIENDLKWRQFRHKADNFNKFKNLC 60
LD++ PE + R + + + +I + RQ R + + + K
Sbjct: 41 LDMESLCA----YPEDAARALDLRKGELRSKDLPGIISTWQELRQLREQIRSLEEEKEAV 96
Query: 61 SKVIGEKMKAKEPVGDSS-------------------------------------TLPGN 83
++ + + ++ LP N
Sbjct: 97 TEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLEEQFYLRALRLP-N 155
Query: 84 HLHPSVPVSNNEDENGIVRTKG-----DTEVRKKYSHVDLITMIDGVDSEAGAIVAGGRG 138
HP VPV + E + ++ G + R H+++ +D + + + V+G R
Sbjct: 156 QTHPDVPVGD-ESQARVLHVVGDKPAFSFQPR---GHLEIAEKLDIIRQKRLSHVSGHRS 211
Query: 139 YFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGK 198
Y+L+G LQ GLV + L+K I +G+TP+ P +R V + I
Sbjct: 212 YYLRGAGALLQHGLVNFTLNKLIHRGFTPMTVPDLLRGVVFEGCGMTPNAKPSQIYNI-- 269
Query: 199 GEKVGDSAPEKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE----- 253
+ +D L T+E + D + LPIR + STC+R E
Sbjct: 270 ---------DPSRFEDLNLAGTAEVGLAGYFMDHSVAFRDLPIRMVCSSTCYRAETDTGK 320
Query: 254 --------------------------------DLTKS---------IAYRVVNIVSGALN 272
+ + +RV+++ + L
Sbjct: 321 EPWGLYRVHHFTKVEMFGVTGPGLEQSSELLEEFLSLQMEILTELGLHFRVLDMPTQELG 380
Query: 273 HAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATA 332
A +K D+EAW PG G F E+ S SNC D+QSRRL + + + +++F H +NAT
Sbjct: 381 LPAYRKFDIEAWMPGRGRFGEVTSASNCTDFQSRRLHIMF---QTEAGELQFAHTVNATG 437
Query: 333 CATTRVICAILETHQTETG-VRIPDCLRKFVPAVYVNEAGEIPFVKTAP 380
CA R++ A+LE++Q + G V +P L+ ++ + +P P
Sbjct: 438 CAVPRLLIALLESYQQKDGSVLVPPALQPYLGTDRITTPTHVPLQYIGP 486
>1ses_A Seryl-tRNA synthetase; ligase; HET: AHX AMP; 2.50A {Thermus
thermophilus} SCOP: a.2.7.1 d.104.1.1 PDB: 1ser_A*
1set_A* 1sry_A
Length = 421
Score = 254 bits (652), Expect = 2e-81
Identities = 87/440 (19%), Positives = 171/440 (38%), Gaps = 109/440 (24%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSK 62
+DL R +PE + +++ ++L + ++ D + ++ + + +N +K
Sbjct: 2 VDLKRLRQ----EPEVFHRAIREKGVALDL-EALLALDREVQELKKRLQEVQTERNQVAK 56
Query: 63 VIGEKMKAKEP--------VGDS-------------------STLPGNHLHPSVPVSNNE 95
+ + ++ +G+ +P P PV E
Sbjct: 57 RVPKAPPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVP-LPPWPGAPVGGEE 115
Query: 96 DENGIVRTKG-----DTEVRKKYSHVDLITMIDGVDSEAGAIVAGGRGYFLKGPAVCLQV 150
N ++ G HV L+ + + V+G R Y LKG ++
Sbjct: 116 A-NREIKRVGGPPEFSFPPL---DHVALMEKNGWWE-PRISQVSGSRSYALKGDLALYEL 170
Query: 151 GLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAPEKD 210
L+++A+ +G+ P+ P + R++ + ++++ +
Sbjct: 171 ALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAI--------------- 215
Query: 211 ELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE----------------- 253
D YL T+E + A+H LP +LP+RY G + FR E
Sbjct: 216 AETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQF 275
Query: 254 ---------------------DLTKS---------IAYRVVNIVSGALNHAAAKKLDLEA 283
+L ++ + YR+V + +G + +++D+E
Sbjct: 276 HKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEV 335
Query: 284 WFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVICAIL 343
+ P G +RE SCS LD+Q+RR +RY + ++ + + LN TA AT R++ +L
Sbjct: 336 YLPSEGRYRETHSCSALLDWQARRANLRY---RDPEGRVRYAYTLNNTALATPRILAMLL 392
Query: 344 ETHQTETG-VRIPDCLRKFV 362
E HQ + G VR+P L ++
Sbjct: 393 ENHQLQDGRVRVPQALIPYM 412
>3err_A Fusion protein of microtubule binding domain from mouse cytoplasmic
dynein and seryl-tRNA...; coiled coil, ligase; HET: AMP;
2.27A {Mus musculus}
Length = 536
Score = 239 bits (612), Expect = 3e-74
Identities = 91/454 (20%), Positives = 163/454 (35%), Gaps = 121/454 (26%)
Query: 1 MVLDLDLFRTEKGGDPEKVRKNQKDR-FKNV------ELVDKVIENDLKWRQFRHKADNF 53
+ L L T D +++R F E + I +K + + N+
Sbjct: 97 IALLLGESTT----DWKQIRSIIMRENFIPTIVNFSAEEISDAIREKMKKNYMSNPSYNY 152
Query: 54 NKFKNLCSKVIGEKMKAKEPVGDSS--------------------------------TLP 81
N S G +K + + +P
Sbjct: 153 EI-VNRASLAAGPMVKWAIAQLNYADMLKRVEPLRNELQKLEDDAKDNQQKLEALLLQVP 211
Query: 82 GNHLHPSVPVSNNEDENGIVRTKG-----DTEVRKKYSHVDLITMIDGVDSEAGAIVAGG 136
P PV E N ++ G HV L+ + + V+G
Sbjct: 212 -LPPWPGAPVGGEEA-NREIKRVGGPPEFSFPPL---DHVALMEKNGWWE-PRISQVSGS 265
Query: 137 RGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVI 196
R Y LKG ++ L+++A+ +G+ P+ P + R++ + ++++ +
Sbjct: 266 RSYALKGDLALYELALLRFAMDFMARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAI- 324
Query: 197 GKGEKVGDSAPEKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE--- 253
D YL T+E + A+H LP +LP+RY G + FR E
Sbjct: 325 --------------AETDLYLTGTAEVVLNALHSGEILPYEALPLRYAGYAPAFRSEAGS 370
Query: 254 -----------------------------------DLTKS---------IAYRVVNIVSG 269
+L ++ + YR+V + +G
Sbjct: 371 FGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATG 430
Query: 270 ALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLN 329
+ +++D+E + P G +RE SCS LD+Q+RR +RY + ++ + + LN
Sbjct: 431 DMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRY---RDPEGRVRYAYTLN 487
Query: 330 ATACATTRVICAILETHQTETG-VRIPDCLRKFV 362
TA AT R++ +LE HQ + G VR+P L ++
Sbjct: 488 NTALATPRILAMLLENHQLQDGRVRVPQALIPYM 521
>2dq3_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics,
NPPSFA, nationa on protein structural and functional
analyses; HET: SSA; 3.00A {Aquifex aeolicus}
Length = 425
Score = 233 bits (596), Expect = 5e-73
Identities = 122/440 (27%), Positives = 192/440 (43%), Gaps = 106/440 (24%)
Query: 3 LDLDLFRTEKGGDPEKVRKNQKDR-FKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCS 61
+D++L R P+ V++ R + V LVDKV+E D + R+ + + +N S
Sbjct: 2 IDINLIRE----KPDYVKERLATRDKELVSLVDKVLELDKRRREIIKRLEALRSERNKLS 57
Query: 62 KVIGEKMKAKEP----------VGDS-------------------STLPGNHLHPSVPVS 92
K IG+ + + + + +P N HPSVPV
Sbjct: 58 KEIGKLKREGKDTTEIQNRVKELKEEIDRLEEELRKVEEELKNTLLWIP-NLPHPSVPVG 116
Query: 93 NNEDENGIVRTKG-----DTEVRKKYSHVDLITMIDGVDSEAGAIVAGGRGYFLKGPAVC 147
+E +N VR G D E + H ++ + +D + GA ++G R + G
Sbjct: 117 EDEKDNVEVRRWGEPRKFDFEPK---PHWEIGERLGILDFKRGAKLSGSRFTVIAGWGAR 173
Query: 148 LQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKVGDSAP 207
L+ L+ + L +KGY + P ++ E++ QL +F+E+LYK
Sbjct: 174 LERALINFMLDLHTKKGYKEICPPHLVKPEILIGTGQLPKFEEDLYKC------------ 221
Query: 208 EKDELDDKYLIATSEQPICAVHRDSWLPEASLPIRYLGVSTCFRQE-------------- 253
E D+ YLI T+E P+ ++R+ L E +LPI + C+R+E
Sbjct: 222 ---ERDNLYLIPTAEVPLTNLYREEILKEENLPIYLTAYTPCYRREAGAYGKDIRGIIRQ 278
Query: 254 ----------------------DLTKS---------IAYRVVNIVSGALNHAAAKKLDLE 282
L K + YRVV + +G L +AAK D+E
Sbjct: 279 HQFDKVELVKIVHPDTSYDELEKLVKDAEEVLQLLGLPYRVVELCTGDLGFSAAKTYDIE 338
Query: 283 AWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVICAI 342
WFP +RE+ SCSNC D+Q+RR+ R+ +K K FVH LN + A R + AI
Sbjct: 339 VWFPSQNKYREISSCSNCEDFQARRMNTRFKDSK--TGKNRFVHTLNGSGLAVGRTLAAI 396
Query: 343 LETHQTETG-VRIPDCLRKF 361
LE +Q E G V +P+ LR +
Sbjct: 397 LENYQQEDGSVVVPEVLRDY 416
>3mf2_A BLL0957 protein; aminoacyl-tRNA synthetase, seryl-tRNA synthetase,
zinc ION, amino acid:[carrier protein] ligase; HET: AMP;
2.15A {Bradyrhizobium japonicum} PDB: 3mey_A* 3mf1_A*
3pzc_A*
Length = 346
Score = 140 bits (354), Expect = 2e-38
Identities = 46/347 (13%), Positives = 87/347 (25%), Gaps = 80/347 (23%)
Query: 77 SSTLPGNHLHPSVPVSNNEDENGIVRTKGDTEVRKKYSHVDLITMIDGVDSEAGAIVAGG 136
SS +H VP + ++ DT + +D + + G
Sbjct: 3 SSHHHHHHSSGLVP-RGSHMNIAVLPNSPDT-------APQIADPLDHLA-DKLFHSMGS 53
Query: 137 RGYFLKGPAVCLQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVI 196
G + + V + ++ E G L P M + +++ L F L V
Sbjct: 54 DGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVC 113
Query: 197 GKGEKVGDSAPEKDELDDK------------YLIATSEQPICAVHRDSWLPEASLPIRYL 244
G + D L + P+ + +R+
Sbjct: 114 GLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPK-GGLRFD 172
Query: 245 GVSTCFRQE---------------------------------DLTKSIA------YRVVN 265
+ CFR+E ++IA +RV
Sbjct: 173 VAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDY 232
Query: 266 ----------IVSGALNHAAAKKLDLEAWFPGSGAFRELVSCSNCLDYQSRRLLVRYGQT 315
+ K +L +S + ++ ++
Sbjct: 233 ASDPFFGRVGQMKAVSQKQQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANG 292
Query: 316 KKMNEKIEFVHMLNATACATTRVICAILETHQTETGVRIPDCLRKFV 362
E H A R+ A+ TH T+ P +R +
Sbjct: 293 -------EPAHT-GCVAFGMDRLAVAMFHTHGTDLS-AWPAKVRDIL 330
>2cja_A Seryl-tRNA synthetase; ligase, zinc ION; HET: MSE ATP; 2.2A
{Methanosarcina barkeri} PDB: 2cim_A* 2cj9_A* 2cjb_A
Length = 522
Score = 130 bits (327), Expect = 1e-33
Identities = 56/427 (13%), Positives = 101/427 (23%), Gaps = 96/427 (22%)
Query: 17 EKVRKNQKDRFKNVELVDKVIENDLKWRQFRHKADNFNKFKNLCSKV-----IGEKMKAK 71
E + K K + +E+ +I+ K +N+ + +GE
Sbjct: 103 EALGKKYKIGIRGIEVESFIIKVPADHELRMLKVPYIKSMENIEGGIQLELEVGEAEMKN 162
Query: 72 EPVGDSSTLPGNHLHPSVPVSNNEDENGIVRTKGDTEVRKKYSHVDLITMIDGVDSEAGA 131
TL + + + E N + + R+ H + E
Sbjct: 163 RVPDRILTLLEEKIEAAQYGAKAEHWNLLWQ-------REPMEHPFKEDPTQAMMKEGWL 215
Query: 132 IVAGGRG-YFLKGPAVCLQVGLVQYALSKWIEK-GYTPLYTPFFMRKEVMQEVAQLAQFD 189
RG + + + + L + +E GY + P + EV +
Sbjct: 216 KRGSSRGQWIHGPQSARIFRTFEKIVLEELLEPLGYREMIFPKLVTWEVWMKSGHAKGVY 275
Query: 190 EELYKVIG------------------KGEKVGDSAPEKDELDDKYLIATSEQPICAVHRD 231
E+Y V E EK + P
Sbjct: 276 PEIYYVCPPQTRDPDYWEEVADYYKVTHEVPTKLIKEKIAEPIGGMCYAQCPPFWMYVAG 335
Query: 232 SWLPEASLPIRYLGVS-TCFRQE--------------------------------DLTKS 258
LP +P++ S T R E +L
Sbjct: 336 ETLPNEEIPVKVFDRSGTSHRYESGGIHGIERVDEFHRIEIVWIGTKEEVLKCAEELHDR 395
Query: 259 IA----------YRVVNI---------VSGALNHAAAKKLDLEAWFP---GSGAFRELVS 296
+R + + G D EA P G + E +
Sbjct: 396 YMHIFNDILDIEWRKARVTPWFMAQEGLLGLAEENTVGTTDYEACLPYRGPDGEWLEFQN 455
Query: 297 CSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNATACATTRVICAILETHQTETGVRIPD 356
S D + V+ + + + + R L + P+
Sbjct: 456 VSINGDKYPKGFNVKL-------QSGDELW-SGCSGVGLERWAAVFLAQKGLDPA-NWPE 506
Query: 357 CLRKFVP 363
R V
Sbjct: 507 EFRNRVG 513
>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 = 53.9 bits (129), Expect = 7e-08
Identities = 53/362 (14%), Positives = 109/362 (30%), Gaps = 134/362 (37%)
Query: 98 NGIVRTKGDTEVRKKYSH-VDLITMIDGVDSEAGAIVAGGRGYFLKGPAVCLQVGLVQ-- 154
+ ++RT D E K ++ ++++ ++ + + Y L P C +G++Q
Sbjct: 196 SELIRTTLDAE--KVFTQGLNILEWLENPSN------TPDKDYLLSIPISCPLIGVIQLA 247
Query: 155 -YALSKWIEKGYTPLYTPFFMRKEVMQEVAQLAQFDEELYKVIGKGEKV--------GDS 205
Y ++ + G+TP + L G + + DS
Sbjct: 248 HYVVTAKL-LGFTP------------------GELRSYLKGATGHSQGLVTAVAIAETDS 288
Query: 206 APEKDELDDKYL-----IATSEQ---PICA----VHRDSWLPEASLP-----IRYLGVST 248
K + I P + + DS +P I ++
Sbjct: 289 WESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS--NLTQ 346
Query: 249 CFRQEDLTK-----------SIAYRVVN-----IVSGALNHAAAKKLDLEAWFPGSGAFR 292
Q+ + K I+ +VN +VSG L + R
Sbjct: 347 EQVQDYVNKTNSHLPAGKQVEIS--LVNGAKNLVVSG---PPQ----SLYGL---NLTLR 394
Query: 293 ELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFV----------H---MLNATACATTRVI 339
+ + LD QSR + + + K++F H ++ A+ ++
Sbjct: 395 K-AKAPSGLD-QSR---IPFSE-----RKLKFSNRFLPVASPFHSHLLVPASDLINKDLV 444
Query: 340 CAILETHQTETGVRIPDCLRKFVPAVYVNEAGE-------------IPFVKTAPID-EEE 385
+ + + ++IP VY G + + P+ E
Sbjct: 445 KNNVSFNAKD--IQIP---------VYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETT 493
Query: 386 TK 387
T+
Sbjct: 494 TQ 495
Score = 47.7 bits (113), Expect = 6e-06
Identities = 49/249 (19%), Positives = 78/249 (31%), Gaps = 92/249 (36%)
Query: 91 VSNNEDENGIVRT-KGDTEVRKKYSHVDLITMIDG-VDSEA--GAIVAGGRGYFLKGPAV 146
V NN I + +R+ YS + T++DG + +E I Y +
Sbjct: 1665 VINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKG 1724
Query: 147 CL------QVGL--VQYALSK-WIEKGYTPL-----------YTPFFMRKEVMQEVAQLA 186
L Q L ++ A + KG P Y A LA
Sbjct: 1725 LLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYA------------A-LA 1771
Query: 187 ------QFDEELYKVIGK-GEKVGDSAPEKDELDDKYLIATSEQPICAVHRDSWLPEASL 239
E L +V+ G + + P +DEL S + A++
Sbjct: 1772 SLADVMSI-ESLVEVVFYRGMTMQVAVP-RDEL------GRSNYGMIAIN---------- 1813
Query: 240 PIRYLGVSTCFRQEDLT---KSIAYR------VVN--------IVSG----------ALN 272
P R V+ F QE L + + R +VN + +G LN
Sbjct: 1814 PGR---VAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLN 1870
Query: 273 HAAAKKLDL 281
+K+D+
Sbjct: 1871 FIKLQKIDI 1879
Score = 43.1 bits (101), Expect = 1e-04
Identities = 51/271 (18%), Positives = 80/271 (29%), Gaps = 82/271 (30%)
Query: 148 LQVGLVQYALSKWIEKGYTPLYTPFFMRKEVMQE--VAQLAQFDEELYKVIGKGEKVGDS 205
L G +++ L P T F +QE L + E D
Sbjct: 11 LSHGSLEHVLL-------VP--TASFFIASQLQEQFNKILPEPTEGF---------AADD 52
Query: 206 APE-KDELDDKYL--IATSEQPICAVHRDSWLPEASLP---IRYLG-------VSTCFRQ 252
P EL K+L +++ +P D L L YL + ++
Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVL-NLCLTEFENCYLEGNDIHALAAKLLQE 111
Query: 253 EDLT----KSI--AYRVVNIVSG---------AL-NHAAAKKLDLEAWFPGSGA----FR 292
D T K + Y I++ AL L A F G G F
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFE 171
Query: 293 ELVSCSNCLDYQSRRLLVRYGQTKKMNEKIEFVHMLNAT--ACATTRVICAILETHQTET 350
EL L YQ+ +LV + + T T + + T
Sbjct: 172 ELRD----L-YQTYHVLVG-----------DLIKFSAETLSELIRTTLDAEKVFTQ---- 211
Query: 351 GVRIPDCLRKFVPAVYVNEAGEIPFVKTAPI 381
G+ I + L P + + ++ + PI
Sbjct: 212 GLNILEWLEN--P----SNTPDKDYLLSIPI 236
>3klo_A Transcriptional regulator VPST; REC domain, HTH domain,
DNA-binding, transcription regulation; HET: C2E TAR;
2.80A {Vibrio cholerae} PDB: 3kln_A*
Length = 225
Score = 29.9 bits (68), Expect = 1.0
Identities = 3/45 (6%), Positives = 11/45 (24%)
Query: 98 NGIVRTKGDTEVRKKYSHVDLITMIDGVDSEAGAIVAGGRGYFLK 142
+ + + + +I ++ + G F
Sbjct: 68 DVLTDYSSFKHISCPDAKEVIINCPQDIEHKLLFKWNNLAGVFYI 112
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.7 bits (66), Expect = 1.2
Identities = 12/61 (19%), Positives = 32/61 (52%), Gaps = 10/61 (16%)
Query: 15 DPEKVRKNQKDRFKNVELVDKVIENDL-KWR-QFRHKADNFNKFKNLCSKVIGEKM-KAK 71
+PE +RK ++++ K ++ +D + +WR + + + +N+ ++ E++ K K
Sbjct: 83 EPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQS-------EQVEKNK 135
Query: 72 E 72
Sbjct: 136 I 136
>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 = 27.2 bits (59), Expect = 5.6
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 9/28 (32%)
Query: 180 QEVAQLAQFDEELYKVIGKGEKVGDSAP 207
Q + +L Q +LY DSAP
Sbjct: 20 QALKKL-QASLKLY--------ADDSAP 38
>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 = 28.3 bits (62), Expect = 6.0
Identities = 27/161 (16%), Positives = 48/161 (29%), Gaps = 44/161 (27%)
Query: 5 LDLFRTEKGGDPEKVRKNQKDRFKNVELVD--KVIENDLKWRQFRHKADNFNKFKNLCSK 62
+D + K D + + D++ + K IE+ + FR +F F
Sbjct: 450 VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR-F------ 502
Query: 63 VIGEKMKAKEPVGDSSTLPGNHLHPSVPVSNNEDENGIVRTKGDTEVRKKYSHVDLITMI 122
+ +K++ + G+ L+ T + K Y I
Sbjct: 503 -LEQKIRH---DSTAWNASGSILN----------------TLQQLKFYKPY-----ICDN 537
Query: 123 DGVDSE-AGAIVAGGRGYFLKGPAVCLQVG----LVQYALS 158
D AI+ FL L L++ AL
Sbjct: 538 DPKYERLVNAIL-----DFLPKIEENLICSKYTDLLRIALM 573
>3seb_A SEB, staphylococcal enterotoxin B; superantigen; 1.48A
{Staphylococcus aureus} SCOP: b.40.2.2 d.15.6.1 PDB:
1se4_A* 1d5x_C* 1d5z_C* 1d6e_C* 1sbb_B 1se3_A* 1d5m_C*
2seb_D* 3r8b_A 1goz_A 3gp7_A 1seb_D
Length = 238
Score = 27.4 bits (60), Expect = 6.8
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 27 FKNVELVDKVIENDLKWRQFRHKADNFNKFK-NLCSKVIGEKMKAKE 72
NV+ +D+ + DL + K N++ + +K + +K K K
Sbjct: 35 AINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKY 81
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 0.135 0.395
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,179,358
Number of extensions: 376408
Number of successful extensions: 908
Number of sequences better than 10.0: 1
Number of HSP's gapped: 864
Number of HSP's successfully gapped: 39
Length of query: 399
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 303
Effective length of database: 4,021,377
Effective search space: 1218477231
Effective search space used: 1218477231
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 (26.2 bits)