RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780834|ref|YP_003065247.1| DNA primase [Candidatus
Liberibacter asiaticus str. psy62]
(648 letters)
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication,
transferase; HET: DNA; 2.00A {Aquifex aeolicus}
Length = 407
Score = 219 bits (559), Expect = 1e-57
Identities = 138/428 (32%), Positives = 204/428 (47%), Gaps = 37/428 (8%)
Query: 6 DFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCF 65
I +L I I ++I +Y++ ++ +N Y CPFH + TPSF+ + SK + CF
Sbjct: 5 SDIDELRREIDIVDVISEYLNLEKVGSN-----YRTNCPFHPDDTPSFYVSPSKQIFKCF 59
Query: 66 SCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVAT 125
C V GD + F+S S+ E+ LA G L + ++K + ++
Sbjct: 60 GCGVGGDAIKFVSLYEDISYFEAALELAKRYGKKLDLEKISKDEKVYV------ALDRVC 113
Query: 126 DFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIE 185
DF+ SL R+ Y+ RGID F LGYAP S ++ L++ E +
Sbjct: 114 DFYRESLLKNREAS--EYVKSRGIDPKVARKFDLGYAPSSEALVK-VLKENDLLEAYLET 170
Query: 186 AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKG 245
LL D F R++ PI+ RG+VI FGGR + + +S KY+NSP++ +F KG
Sbjct: 171 KNLLSPTKGV--YRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVFKKG 228
Query: 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEY 305
+NL+ + A Y F ILVEGY D+L L G++NVV+ LGTALT+
Sbjct: 229 ENLFGLYEAKEY----------IKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQN 278
Query: 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365
Q LL K + ++ + +DGDD G +A AI L G V V L G DPD FI+
Sbjct: 279 QANLLSKFTKKVYILYDGDDAGRKAMKSAIP---LLLSAGVEVYPVYLPEGYDPDEFIKE 335
Query: 366 YGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYS 425
+GK +LI S L + L K EN T + R + I D R+ +
Sbjct: 336 FGKEELRRLINSSGELFETLIKTARENLEEKTREFRYY--------LGFISDGVRRFALA 387
Query: 426 QAIRDRLQ 433
+ +
Sbjct: 388 SEFHTKYK 395
>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA
polymerase, replication protein; HET: DNA; 1.60A
{Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A*
3b39_A*
Length = 338
Score = 210 bits (536), Expect = 6e-55
Identities = 110/321 (34%), Positives = 177/321 (55%), Gaps = 12/321 (3%)
Query: 117 LIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQK 176
L +L++ F+ SL+ YL++RG+ I F +G+AP ++ +
Sbjct: 21 LYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGN 80
Query: 177 GFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNS 236
+ + +I+AG+L+ D SYDRFR R++FPIR RG+VI FGGR L ++ KYLNS
Sbjct: 81 PENRQSLIDAGMLVTNDQG-RSYDRFRERVMFPIRDKRGRVIGFGGRVLGN-DTPKYLNS 138
Query: 237 PETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVS 296
PET +FHKG+ LY + + +++VEGYMDV++L Q G+ V+
Sbjct: 139 PETDIFHKGRQLYGLY----------EAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVA 188
Query: 297 SLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG 356
SLGT+ T ++LL++ + ++ C+DGD G AA++A++ L ++ G ++ F+ L G
Sbjct: 189 SLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDG 248
Query: 357 EDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIK 416
EDPD+ +R GK AFE + +++PL L+ +TPD RA L I+ +
Sbjct: 249 EDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVP 308
Query: 417 DQKLRYYYSQAIRDRLQQLFQ 437
+ LR Y Q + ++L L
Sbjct: 309 GETLRIYLRQELGNKLGILDD 329
>1d0q_A DNA primase; zinc-binding motif, protein; HET: DNA; 1.71A {Bacillus
stearothermophilus} SCOP: g.41.3.2
Length = 103
Score = 92.7 bits (230), Expect = 2e-19
Identities = 39/102 (38%), Positives = 58/102 (56%), Gaps = 5/102 (4%)
Query: 3 YPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFY 62
P + I+ + + I ++IG+YV R+ N Y+ CPFH EKTPSF + K +
Sbjct: 5 IPEETIEAIRRGVDIVDVIGEYVQLKRQGRN-----YFGLCPFHGEKTPSFSVSPEKQIF 59
Query: 63 YCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVD 104
+CF C G+ +FL + G F+E+ +RLAA AGV L V +
Sbjct: 60 HCFGCGAGGNAFTFLMDIEGIPFVEAAKRLAAKAGVDLSVYE 101
>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET:
DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11
e.13.1.2
Length = 503
Score = 84.6 bits (208), Expect = 7e-17
Identities = 33/211 (15%), Positives = 67/211 (31%), Gaps = 40/211 (18%)
Query: 171 EHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGES 230
L +G S+E +AG I + + R G +++ R K +
Sbjct: 16 SALTARGISKETCQKAGYWIAKVDG-------VMYQVADYRDQNGNIVSQKVRDKDK--N 66
Query: 231 VKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAG 290
K S K L+ N I++ EG +D+L++ +
Sbjct: 67 FKTTGSH------KSDALFGKHLW--------------NGGKKIVVTEGEIDMLTVMELQ 106
Query: 291 VQNVVSSLGTALTEYQLRLLWKLSP------RIVLCFDGDDPGLRAAYKAIDLVLCHLIP 344
+ +I+L FD D+ G +A +A ++P
Sbjct: 107 DCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEA-----AQVLP 161
Query: 345 GNRVNFVLLSRGEDPDSFIRCYGKTAFEKLI 375
+V +L + + + + + E++
Sbjct: 162 AGKVRVAVLPCKDANECHLNGHDREIMEQVW 192
>1t6t_1 Putative protein; structural genomics, PSI, protein structure
initiative, midwest center for structural genomics,
MCSG, unknown function; 1.80A {Aquifex aeolicus VF5}
SCOP: c.136.1.1
Length = 118
Score = 80.1 bits (197), Expect = 1e-15
Identities = 29/129 (22%), Positives = 53/129 (41%), Gaps = 19/129 (14%)
Query: 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEY 305
K N K++++ S +ILVEG D +L + ++NV+ G +
Sbjct: 3 KEPRNLSEW--------IKELKKASREAVILVEGKNDKKALSKFSIKNVIDLSGKRYADV 54
Query: 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365
L K +++L FD D G R K +L+ G V+ E+ +F++
Sbjct: 55 VDMLEGK-WEKVILLFDLDTHGERINQKMKELLSSQ---GFLVD-------ENFRNFLKK 103
Query: 366 YGKTAFEKL 374
+ E++
Sbjct: 104 WNIIHIEEI 112
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; HET: MES; 1.30A {Geobacillus
stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A*
Length = 119
Score = 66.5 bits (162), Expect = 2e-11
Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 3/68 (4%)
Query: 274 IILVEGYMDVLSLCQAGVQNVVSSL-GTALTEYQLRLLWKLS--PRIVLCFDGDDPGLRA 330
+I+VEG D + + VV +++ +L L + L D D+ G +
Sbjct: 7 VIIVEGRSDKQKVAAVLNEPVVIVCTNGTISDARLEELADELEGYDVYLLADADEAGEKL 66
Query: 331 AYKAIDLV 338
+ +
Sbjct: 67 RRQFRRMF 74
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA
replication, DNA- directed RNA polymerase, primosome,
late protein; HET: DNA; 2.90A {Enterobacteria phage T7}
SCOP: e.13.1.2 g.41.3.2
Length = 255
Score = 64.2 bits (155), Expect = 8e-11
Identities = 36/340 (10%), Positives = 73/340 (21%), Gaps = 112/340 (32%)
Query: 49 KTPSFHCNDSKGF-------YYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLP 101
P +C S G +C+ C
Sbjct: 14 HIPCDNCGSSDGNSLFSDGHTFCYVCEKWTA----------------------------- 44
Query: 102 VVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGY 161
++ + R ++ + L RGI +
Sbjct: 45 ------GNEDTKERASKRKPSGGKPGTYNVWNFGESNGRYSALTARGISKETCQKAGYWI 98
Query: 162 APDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFG 221
+ + R G +++
Sbjct: 99 ------------------------------------AKVDGVMYQVADYRDQNGNIVSQK 122
Query: 222 GRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYM 281
R K K+ F L K I++ EG +
Sbjct: 123 VRDKDK----------NFKTTGSHKSDALFGKHLWNGGK------------KIVVTEGEI 160
Query: 282 DVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSP------RIVLCFDGDDPGLRAAYKAI 335
D+L++ + + +I+L FD D+ G +A +A
Sbjct: 161 DMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAA 220
Query: 336 DLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLI 375
++P +V +L +D + + +
Sbjct: 221 Q-----VLPAGKVRVAVLP-CKDANECHLNGHDREIMEQV 254
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 53.0 bits (127), Expect = 2e-07
Identities = 107/598 (17%), Positives = 180/598 (30%), Gaps = 218/598 (36%)
Query: 121 IEVATD-FFHHS-LKNARDKRLHYYLDERGID---SHAIEM---FKLGY-----APDSRY 167
+ V T FF S L+ +K L + D + E+ F LGY P
Sbjct: 20 LLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF-LGYVSSLVEPSKVG 78
Query: 168 SLREHLRQ--KGFSEEKIIE--------AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQV 217
+ L F E +E A LL + D + LI ++
Sbjct: 79 QFDQVLNLCLTEF-ENCYLEGNDIHALAAKLLQENDTTLVK----TKELI---KN----- 125
Query: 218 IAFGGRTLSKGESVKYLNSPETILFH---KGK-NLYNFFG----ALNYLQ---------K 260
R ++K K + LF +G L FG +Y +
Sbjct: 126 -YITARIMAKRPFDK---KSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYH 181
Query: 261 SIRKD-VRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSL----GTALTEYQLRLLWKLSP 315
+ D ++ ++ + L+ +D + G+ N++ L T +Y L LS
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKVFTQGL-NILEWLENPSNTPDKDY----L--LSI 234
Query: 316 RIVLCFDGDDP--GLRAAYKAIDL----VLCHLI---PGN-RVNF-------------VL 352
I P G+ I L V L+ PG R V
Sbjct: 235 PISC------PLIGV------IQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVA 282
Query: 353 LSRGEDPDSFIRCYGKTAFEKL--I-VESLPLVDMLWKRETENRSFNTPDERAELEIHLK 409
++ + +SF + A L I V E + P +
Sbjct: 283 IAETDSWESFFVS-VRKAITVLFFIGVRCY---------EAYPNTSLPPSILED------ 326
Query: 410 NCINHIKDQK---LRYYYSQAIRD-RLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQR 465
+ + + L +I + +Q+ Q Y+ + N H P+ +
Sbjct: 327 -SLENNEGVPSPML------SISNLTQEQV-QDYVNKT---------N-SHL----PAGK 364
Query: 466 LMQSSLVKGK----LSKKP-SLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWS 520
++ SLV G +S P SL L L P+ L +Q + I + +KL
Sbjct: 365 QVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGL-DQ----SRIPFSE---RKL-- 414
Query: 521 FLFSDFVEQKYFLP--------------EEIHQRLCERGF-------------------- 546
F + FLP + I++ L +
Sbjct: 415 ----KFSNR--FLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL 468
Query: 547 ----GELLKQLDRQV-RDAGLWSATTEAN---IVDVRQGYQQALALYKRFRLLSRQKE 596
G + +++ + R W TT+ I+D G L + L R K+
Sbjct: 469 RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGV-----LTHRNKD 521
Score = 50.7 bits (121), Expect = 1e-06
Identities = 76/499 (15%), Positives = 130/499 (26%), Gaps = 208/499 (41%)
Query: 5 RDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYC 64
+++ IH + L+ + T + Y
Sbjct: 93 NCYLEGNDIHALAAKLLQ-----ENDTTLVKTKE-LIKN------------------YI- 127
Query: 65 FSCHVKGDHLSFL--SALLGCSFIESVQ----RLAAIAG------------VPL-----P 101
+ + SAL +V +L AI G L
Sbjct: 128 TARIMAKRPFDKKSNSALF-----RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV 182
Query: 102 VVDPKIEKKEKIQTDLIRLIEVATDFFHHS------LKNARDKR---------------- 139
+V I+ + ++LIR A F L+N
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLEN-PSNTPDKDYLLSIPISCPLI 241
Query: 140 -----LHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLR-QKGFSEEKIIEAGLLIDGD 193
HY + + LG+ P LR +L+ G S + ++ A +
Sbjct: 242 GVIQLAHYV-----VTAKL-----LGFTPG---ELRSYLKGATGHS-QGLVTAVAI---- 283
Query: 194 NSATSYDRF-RN-----RLIFPIRSSRGQVIAFGGRTLS---------KGE-------SV 231
S++ F + ++F I R A+ +L E S+
Sbjct: 284 AETDSWESFFVSVRKAITVLFFI-GVRCY-EAYPNTSLPPSILEDSLENNEGVPSPMLSI 341
Query: 232 KYLNSPETILFHKGKNLYNFFGALN-YLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAG 290
L + + ++ N +L ++ I LV G
Sbjct: 342 SNLTQEQ---------VQDYVNKTNSHLPAG-----KQVE---ISLVNGA---------- 374
Query: 291 VQN-VVSSLGTALTEYQL-RLLWKLS----------------PRIVLCFDGDD------- 325
+N VVS G + Y L L K + F
Sbjct: 375 -KNLVVS--GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF----LPVASPF 427
Query: 326 --PGLRAAYKAI--DLVLCHL-IPGNRVNF-VLLSR-GEDPDSFIRCYGKTAFEKLIVES 378
L A I DLV ++ + V + G D +R + I E
Sbjct: 428 HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD----LRVLSGS-----ISER 478
Query: 379 LPLVDML------WKRETE 391
+VD + W+ T+
Sbjct: 479 --IVDCIIRLPVKWETTTQ 495
Score = 49.9 bits (119), Expect = 2e-06
Identities = 84/473 (17%), Positives = 130/473 (27%), Gaps = 218/473 (46%)
Query: 3 YPRDFIKDL----------LIHIP--ISNLIGQYVD---W--DRRKTNAVKGDYWACCPF 45
Y + DL LI + Q ++ W + T DY P
Sbjct: 180 Y-HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK--DYLLSIPI 236
Query: 46 HDEKTPSF---------HCNDSKGFYYCFSCHVKGDH----LSFLSALLGCSFIESVQRL 92
S H Y + + G S+L G S Q L
Sbjct: 237 ------SCPLIGVIQLAH--------YVVTAKLLGFTPGELRSYLKGATGHS-----QGL 277
Query: 93 ---AAIA----------------------GV------P---LP--VVDPKIEKKEKIQTD 116
AIA GV P LP +++ +E E + +
Sbjct: 278 VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSP 337
Query: 117 LIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSH-------AIEM------FKLGYAP 163
++ S+ N +++ Y+++ +SH I + + P
Sbjct: 338 ML------------SISNLTQEQVQDYVNK--TNSHLPAGKQVEISLVNGAKNLVVSGPP 383
Query: 164 DSRYSLREHLRQKGFSEEKI-IEAGLLIDGDNSATSYD----RFRNRLIFPIRSSRGQVI 218
S Y L LR K +GL D S + +F NR + P+
Sbjct: 384 QSLYGLNLTLR-------KAKAPSGL----DQSRIPFSERKLKFSNRFL-PV-------- 423
Query: 219 AFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKS---IRKDVRRNS----- 270
SP FH + L + I KD+ +N+
Sbjct: 424 ----------------ASP----FHS-----------HLLVPASDLINKDLVKNNVSFNA 452
Query: 271 SSFIILVEGY-----MDVLSLCQAGVQNVVSSLGTALTEYQLRLLW----KLSPRIVLCF 321
I V Y D+ L ++ + + L + W + +L F
Sbjct: 453 KDIQIPV--YDTFDGSDLRVLS----GSISERIVDCIIR--LPVKWETTTQFKATHILDF 504
Query: 322 D-GDDPGLRAAYKAIDLVLCHLIP---GNRVNFVL---LSRGEDPDSFIRCYG 367
G GL VL H G RV ++ L D D YG
Sbjct: 505 GPGGASGLG--------VLTHRNKDGTGVRV--IVAGTLDINPDDD-----YG 542
Score = 28.4 bits (63), Expect = 5.0
Identities = 32/179 (17%), Positives = 51/179 (28%), Gaps = 76/179 (42%)
Query: 496 AILQEQYQELADIRYDNNELQ---KLW-SFLFSDFV-----------------------E 528
IL E + A ++E +L FL +V E
Sbjct: 39 KILPEPTEGFAA----DDEPTTPAELVGKFL--GYVSSLVEPSKVGQFDQVLNLCLTEFE 92
Query: 529 QKYFLPEEIH---QRLCERGFGELLKQLD----------------RQVRDAGLWSATTE- 568
Y +IH +L + L+K + + ++ L+ A E
Sbjct: 93 NCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG 152
Query: 569 -ANIVDV--RQG----YQQALA-LY---------------KRFRLLSRQKEEIEKQIAQ 604
A +V + QG Y + L LY + L R + EK Q
Sbjct: 153 NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ 211
>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 = 35.3 bits (81), Expect = 0.046
Identities = 10/33 (30%), Positives = 11/33 (33%), Gaps = 1/33 (3%)
Query: 43 CPFHDEKTPSFHCNDSKGFYYCFSC-HVKGDHL 74
CP P S+G C C V D L
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKL 56
>3dwc_A TCMCP-1, metallocarboxypeptidase; cowrin family of
metallocarboxypeptidases, hydrolase; 2.10A {Trypanosoma
cruzi}
Length = 505
Score = 31.2 bits (70), Expect = 0.68
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 3/61 (4%)
Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKR 587
L +H + L+++ ++ V D AN+ ++R+ ++ L +
Sbjct: 44 AAMAELQLHMHDTITAPKIRALIEEAEKSVGD---LEKLQRANLREMRRAWELENLLPEE 100
Query: 588 F 588
F
Sbjct: 101 F 101
>3hoa_A Thermostable carboxypeptidase 1; proline-rich loop, hydrolase;
2.10A {Thermus thermophilus HB27} PDB: 1wgz_A
Length = 509
Score = 30.8 bits (69), Expect = 0.94
Identities = 20/114 (17%), Positives = 40/114 (35%), Gaps = 6/114 (5%)
Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALA---- 583
Q L +HQR+ + GE L++++ S N+ + RQ Y++A A
Sbjct: 45 RQMAALARLLHQRMTDPRIGEWLEKVEGSPLVQDPLSDAA-VNVREWRQAYERARAIPER 103
Query: 584 LYKRFRLLSRQKEEI-EKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEA 636
L + E E+ + +G + ++ E + +
Sbjct: 104 LAVELAQAESEAESFWEEARPRDDWRGFLPYLKRVYALTKEKAEVLFALPPAPG 157
>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 = 30.7 bits (68), Expect = 1.1
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 10/34 (29%)
Query: 304 EYQ-LRLLWKLSPRIVLCFDGDD--PGLRAAYKA 334
E Q L+ KL + L + DD P L A KA
Sbjct: 18 EKQALK---KLQASLKL-Y-ADDSAPAL--AIKA 44
>1wle_A Seryl-tRNA synthetase; ligase; HET: SRP; 1.65A {Bos taurus}
Length = 501
Score = 29.0 bits (64), Expect = 3.1
Identities = 19/112 (16%), Positives = 39/112 (34%), Gaps = 24/112 (21%)
Query: 534 PEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSR 593
PE+ + L R K L I+ +Q+ L ++ R L
Sbjct: 50 PEDAARALDLRKGELRSKDLPG---------------IIST---WQELRQLREQIRSLEE 91
Query: 594 QKEEIEKQIAQVTAKGEAEKTAI------LISILHEVHIQIHQIESQEAMIE 639
+KE + + + + + + L + E+ Q+ + +EA +E
Sbjct: 92 EKEAVTEAVRALVVNQDNSQVQQDPQYQSLRARGREIRKQLTLLYPKEAQLE 143
>1wdu_A TRAS1 ORF2P; four-layered alpha/beta sandwich, RNA binding protein;
2.40A {Bombyx mori} SCOP: d.151.1.1
Length = 245
Score = 28.8 bits (63), Expect = 3.5
Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 9/78 (11%)
Query: 446 YGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLTLINHPA---ILQEQY 502
+G W A+ R + GP R++Q++L + K L A L + A ++QE Y
Sbjct: 2 HGEQWNTTAKVRPKNGPPYRVLQANLQRKK------LATAELAIEAATRKAAIALIQEPY 55
Query: 503 QELADIRYDNNELQKLWS 520
A ++ S
Sbjct: 56 VGGAKSMKGFRGVRVFQS 73
>3hrp_A Uncharacterized protein; NP_812590.1, structural genomics protein
of unknown function, structural genomics; HET: MSE;
1.70A {Bacteroides thetaiotaomicron vpi-5482}
Length = 409
Score = 28.8 bits (64), Expect = 3.6
Identities = 11/68 (16%), Positives = 21/68 (30%), Gaps = 5/68 (7%)
Query: 187 GLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGE-----SVKYLNSPETIL 241
G+ +D D + D F+ + + G V G+ + N P I
Sbjct: 327 GMTVDEDGNFYIVDGFKGYCLRKLDILDGYVSTVAGQVDVASQIDGTPLEATFNYPYDIC 386
Query: 242 FHKGKNLY 249
+ +
Sbjct: 387 YDGEGGYW 394
>1sjj_A Actinin; 3-helix bundle, calponin homology domain, calmodulin-like
domain, actin binding protein, contractIle protein;
20.00A {Gallus gallus} SCOP: i.15.1.1
Length = 863
Score = 28.7 bits (63), Expect = 3.6
Identities = 28/244 (11%), Positives = 73/244 (29%), Gaps = 9/244 (3%)
Query: 371 FEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRD 430
+ + + P + + + + E++ QAI
Sbjct: 487 YLEYAKRAAPFNNWMEGAMEDLQDTFIVHTIEEIQGLTTAHEQFKATLPDADKERQAILG 546
Query: 431 RLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLT 490
++ + T H + + + + + + A
Sbjct: 547 IHNEVSKIVQTYHVNMAG--TNPYTTITPQEINGKWEHVRQLVPRRDQALMEEHARQQQN 604
Query: 491 LINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELL 550
+ I+ E+ ++ + +Q L + + + + L
Sbjct: 605 ERLRKQFGAQANVIGPWIQTKMEEIGRISIEMHGTLEDQLNHLRQYEKSIVNYKPKIDQL 664
Query: 551 KQLDRQVRDAG-LWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKG 609
+ +Q+++A + T + +R G++Q L ++R E+E QI AKG
Sbjct: 665 EGDHQQIQEALIFDNKHTNYTMEHIRVGWEQLLTT------IARTINEVENQILTRDAKG 718
Query: 610 EAEK 613
+++
Sbjct: 719 ISQE 722
>1ka2_A M32 carboxypeptidase; hexxh motif, M32 family, metallopeptidase;
2.20A {Pyrococcus furiosus} SCOP: d.92.1.5 PDB: 1k9x_A
1ka4_A
Length = 499
Score = 28.8 bits (64), Expect = 3.9
Identities = 9/83 (10%), Positives = 26/83 (31%), Gaps = 14/83 (16%)
Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKR 587
+ L H+ L F L+++ + + + + + + A A
Sbjct: 48 VAQGELSVLSHELLLHPEFVNLVEKA----KGLENLNEYERGIVRVLDRSIRIARAFP-- 101
Query: 588 FRLLSRQKEEIEKQIAQVTAKGE 610
E +++++ T+
Sbjct: 102 --------PEFIREVSETTSLAT 116
>3hq2_A Bacillus subtilis M32 carboxypeptidase; hydrolase, metal-binding,
metalloprotease, protease, zinc; 2.90A {Bacillus
subtilis}
Length = 501
Score = 28.8 bits (64), Expect = 3.9
Identities = 8/61 (13%), Positives = 19/61 (31%), Gaps = 3/61 (4%)
Query: 528 EQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKR 587
E L +I EL+ L + D + + ++ Y++ + +
Sbjct: 45 ESIGQLSTDIFNIQTSDRMKELIDVLYERFDDLSEDTK---KAVELAKKEYEENKKIPEA 101
Query: 588 F 588
Sbjct: 102 E 102
>2gz4_A Hypothetical protein ATU1052; structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 1.50A {Agrobacterium tumefaciens str}
SCOP: a.211.1.1
Length = 207
Score = 28.4 bits (63), Expect = 5.5
Identities = 15/89 (16%), Positives = 26/89 (29%), Gaps = 13/89 (14%)
Query: 530 KYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDV--------RQGYQQA 581
+ H + E F + L E I D+ GY+
Sbjct: 51 DHAFTVAQHCLIVETIFCRMCPGATPDEMQMALLHDAPEYVIGDMISPFKSVVGGGYKTV 110
Query: 582 -----LALYKRFRLLSRQKEEIEKQIAQV 605
A++ RF L E++ +I +
Sbjct: 111 EKRLEAAVHLRFGLPPHASRELKDRIKKA 139
>3d5l_A Regulatory protein RECX; PSI-II, NYSGXRC, DNA repair, 10123K,
structural genomics, protein structure initiative; 2.35A
{Lactobacillus reuteri 100-23}
Length = 221
Score = 28.3 bits (63), Expect = 6.3
Identities = 22/123 (17%), Positives = 34/123 (27%), Gaps = 40/123 (32%)
Query: 106 KIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHY-------------YLDERGIDSH 152
++ K ++ I I A A + L Y L E
Sbjct: 39 RLMKGTELDEKQIAAIATADQQ-----AKAYSRMLDYLSYQMRTESDIVKKLKEIDTPEE 93
Query: 153 AIE-----MFKLGYAPDSRYS-----------------LREHLRQKGFSEEKIIEAGLLI 190
+E + D Y+ +R+HLRQKG E I +A
Sbjct: 94 FVEPILKKLRGQQLIDDHAYAASYVRTMINTDLKGPGIIRQHLRQKGIGESDIDDALTQF 153
Query: 191 DGD 193
+
Sbjct: 154 TPE 156
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA
surveillance binds to TRF4P/AIR2P heterodimer; 2.70A
{Saccharomyces cerevisiae}
Length = 83
Score = 28.1 bits (62), Expect = 6.5
Identities = 8/38 (21%), Positives = 12/38 (31%), Gaps = 1/38 (2%)
Query: 38 DYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLS 75
W D+ + YC++C KG H
Sbjct: 23 SIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKG-HFG 59
>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 = 28.2 bits (62), Expect = 6.8
Identities = 17/112 (15%), Positives = 39/112 (34%), Gaps = 34/112 (30%)
Query: 534 PEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSR 593
PE + L +RG E +K +D + L L +R +
Sbjct: 11 PELVKNDLIKRGELEKVKWVD-------------------------EILKLDTEWRTKLK 45
Query: 594 QKEEIE-------KQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMI 638
+ + +I + + + E L++ E+ +I ++E++ +
Sbjct: 46 EINRLRHERNKIAVEIGK--RRKKGEPVDELLAKSREIVKRIGELENEVEEL 95
>1pj3_A NAD-dependent malic enzyme, mitochondrial; oxidative decarboxylase,
oxidoreductase; HET: NAD; 2.10A {Homo sapiens} SCOP:
c.2.1.7 c.58.1.3 PDB: 1pj2_A* 1do8_A* 1pj4_A* 1qr6_A*
1efl_A* 1pjl_A* 1efk_A* 1gz4_A* 1gz3_A*
Length = 564
Score = 27.9 bits (62), Expect = 7.2
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 16/63 (25%)
Query: 397 TPDERAELEIH--LKNCINHIKDQKLRYY--------------YSQAIRDRLQQLFQKYI 440
T ER L + L I Q LR++ Y I++R ++LF + +
Sbjct: 21 TLQERQMLGLQGLLPPKIETQDIQALRFHRNLKKMTSPLEKYIYIMGIQERNEKLFYRIL 80
Query: 441 TEH 443
+
Sbjct: 81 QDD 83
>3i4r_B Nuclear pore complex protein NUP133; protein transport,structural
protein, kinetochore, mRNA transport, nucleus,
phosphoprotein, translocation; 3.53A {Homo sapiens}
Length = 644
Score = 27.5 bits (61), Expect = 9.6
Identities = 16/131 (12%), Positives = 42/131 (32%), Gaps = 16/131 (12%)
Query: 421 RYYYSQAIRDRLQQLFQ-------KYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVK 473
R+Y + R +L ++ H W ++ + L+ + ++
Sbjct: 391 RWYLEKGKRGKLLSQPISQHGQLANFLQAHEHLS--WLHEINSQELEKAHATLLGLANME 448
Query: 474 GKL--SKKPSLREAAL-LLTLINHPAILQEQY----QELADIRYDNNELQKLWSFLFSDF 526
+ KK L + L L +LQE+ ++ + + ++L + +
Sbjct: 449 TRYFAKKKTLLGLSKLAALASDFSEDMLQEKIEEMAEQERFLLHQETLPEQLLAEKQLNL 508
Query: 527 VEQKYFLPEEI 537
++
Sbjct: 509 SAMPVLTAPQL 519
>3e3v_A Regulatory protein RECX; PSI-II, NYSGXRC, structural genomics,
protein structure initiative; 2.04A {Lactobacillus
salivarius UCC118}
Length = 177
Score = 27.6 bits (61), Expect = 9.7
Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 7/63 (11%)
Query: 159 LGYAPDSRYSLREHLRQKGFSEEKI-------IEAGLLIDGDNSATSYDRFRNRLIFPIR 211
L Y +R + + LR E+ I I+ L+ D + + + N +
Sbjct: 28 LSYQLRTRKEVEDKLRSLDIHEDYISEIINKLIDLDLINDKNYAESYVRTMMNTSDKGPK 87
Query: 212 SSR 214
+
Sbjct: 88 VIK 90
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.322 0.139 0.413
Gapped
Lambda K H
0.267 0.0522 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 5,712,998
Number of extensions: 273789
Number of successful extensions: 1143
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1121
Number of HSP's successfully gapped: 47
Length of query: 648
Length of database: 5,693,230
Length adjustment: 98
Effective length of query: 550
Effective length of database: 3,317,318
Effective search space: 1824524900
Effective search space used: 1824524900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (27.4 bits)