RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254781215|ref|YP_003065628.1| putative phage terminase,
large subunit [Candidatus Liberibacter asiaticus str. psy62]
(511 letters)
>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative
initiation, ATP-binding, DNA- binding, hydrolase,
nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB:
3ezk_A*
Length = 592
Score = 59.4 bits (143), Expect = 2e-09
Identities = 65/400 (16%), Positives = 118/400 (29%), Gaps = 57/400 (14%)
Query: 82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWF 141
+ R +GKTT+ A + + +V LA+ + L + + LLP+
Sbjct: 183 CNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKGSMSAEVLD-RTKQAIELLPDF--- 238
Query: 142 EMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEAS 201
L P + L S PD G+ I ++ +
Sbjct: 239 ------LQPGIVEWNKGSIELDNGSS------IGAYASSPDAVRGNSFAM---IYIEDCA 283
Query: 202 GTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIFNKPLDDWKRF---------- 251
P+ + + + R I+ + FY+I+ ++ F
Sbjct: 284 FIPNFHDSWLAIQPVISSGRRSKIIITTTPNGLNHFYDIWTAAVEGKSGFEPYTAIWNSV 343
Query: 252 -QIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNREP 310
+ + D + I G R E F + + I + E
Sbjct: 344 KERLYNDEDIFDDGWQWSIQTINGSSLAQFRQEHTAAF-EGTSGTLISGMKLAVMDFIEV 402
Query: 311 C-----------PDPYAPLIMGCDIAEEGGDNTVV-----VLRRGPVIEHLFDWSKTDLR 354
P+P I D +E G + V + +
Sbjct: 403 TPDDHGFHQFKKPEPDRKYIATLDCSEGRGQDYHALHIIDVTDDVWEQVGVLHSNTISHL 462
Query: 355 TTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEM-LGYHVYRVLGQKRAVDLEFCRNRR 413
+ + + +Y + I+ N+TG L M L Y V+ DL + +R
Sbjct: 463 ILPDIVMRYLVEYNECPVYIELNSTGVSVAKSLYMDLEYE--GVICDSY-TDLGMKQTKR 519
Query: 414 TELHV--KMADWLEFASL-INHSGLIQNLKSLKSFIVPNT 450
T+ + D +E L I+H IQ ++F
Sbjct: 520 TKAVGCSTLKDLIEKDKLIIHHRATIQ---EFRTFSEKGV 556
>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 = 43.4 bits (102), Expect = 1e-04
Identities = 80/555 (14%), Positives = 136/555 (24%), Gaps = 243/555 (43%)
Query: 23 EIKLSFSNFVLHFFPWGEKGTPLEGF-SAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGA 81
E+ F +V + G + ++ ++E D H L + +
Sbjct: 59 ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQEND---TT 115
Query: 82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLL----PN 137
+ + + K + A + S L + + L A +
Sbjct: 116 LVKTKELIKNYITA--RIMAKRPFDKKSNSALFRAVGEGNAQLVA-------IFGGQGNT 166
Query: 138 KHWF-EMQSL-SLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAI 195
+F E++ L + D++ S ++ S + RT T G+ I
Sbjct: 167 DDYFEELRDLYQTYH-VLVGDLIKFS----AETLSELIRT-----TLDAEKVF-TQGLNI 215
Query: 196 IN--DEASGTPDV-------INLGILGFL-------TERNANRFWIMTSNP----RRLSG 235
+ + S TPD I+ ++G + T ++ P L G
Sbjct: 216 LEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVT------AKLLGFTPGELRSYLKG 269
Query: 236 -----------------KFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSD 278
D W+ SF R
Sbjct: 270 ATGHSQGLVTAVAIAET----------DSWE--------------SFFV--SVR------ 297
Query: 279 VTRVEV-------CGQ-FPQQDIDSFIPLNIIEEAL-NREPCPDPYAPLIM----GCDIA 325
+ V C + +P + +P +I+E++L N E P P M
Sbjct: 298 -KAITVLFFIGVRCYEAYPN----TSLPPSILEDSLENNEGVPSP-----MLSISNLTQE 347
Query: 326 --------------EE---------GGDNTVV------------VLR------------- 337
G N VV LR
Sbjct: 348 QVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI 407
Query: 338 ----RGPVIEHLF---------DWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTC 384
R + F L ++ I + + + +A
Sbjct: 408 PFSERKLKFSNRFLPVASPFHSHL----LVPASDLI---NKDLVKNNVSFNAK------- 453
Query: 385 DYLEMLGYHVY--------RVLGQK---RAVDLEFCRNRRTELHVKMADW---LEF-ASL 429
+ VY RVL R VD L V W +F A+
Sbjct: 454 ----DIQIPVYDTFDGSDLRVLSGSISERIVDC------IIRLPV---KWETTTQFKAT- 499
Query: 430 INH---------SGL 435
H SGL
Sbjct: 500 --HILDFGPGGASGL 512
Score = 34.1 bits (78), Expect = 0.078
Identities = 91/534 (17%), Positives = 140/534 (26%), Gaps = 228/534 (42%)
Query: 103 STRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQSL------SLHPAPWYSD 156
STRP L S L+ L L+P +F L L P P ++
Sbjct: 5 STRP------LTLSHGSLEHVL---------LVPTASFFIASQLQEQFNKIL-PEP--TE 46
Query: 157 VLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDEASG-TPDVINLGILG-- 213
D + + E F+G+ +++ G V+NL L
Sbjct: 47 ----GFAADDEPTT------PAELVGKFLGYV----SSLVEPSKVGQFDQVLNL-CLTEF 91
Query: 214 ---FL-----------------TERNANRFWI--------MTSNPRR------L-----S 234
+L T + I M P L
Sbjct: 92 ENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGE 151
Query: 235 GKF--YEIF----NKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYG--LDSDVTR-VEVC 285
G IF N DD+ F+ + R + +I L + ++
Sbjct: 152 GNAQLVAIFGGQGN--TDDY--FE-ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAE 206
Query: 286 GQFPQQDIDSFIPLNIIEEALNREPCPD-PY---A----PLI--------------MGCD 323
F Q LNI+E N PD Y PLI +G
Sbjct: 207 KVFTQG-------LNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFT 259
Query: 324 IAEEGGDNTVVVLRR----------GPVI----------EHLFDWSKTDLRTTNNKISGL 363
E LR G V E F + + L
Sbjct: 260 PGE---------LRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITV-------L 303
Query: 364 ----VEKYR-------PDAIIIDA--NNTGARTCDYLEMLGYHVYRVLGQKRAVD--LEF 408
V Y P +I+ D+ NN G + ML + L Q+ V +
Sbjct: 304 FFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSP----ML--SI-SNLTQE-QVQDYVNK 355
Query: 409 C-----RNRRTELHVKMADWLEFASLINHSGLIQNLKSLKSFIVPNTGE------LAIES 457
++ + + SL+N K+ +V +G L +
Sbjct: 356 TNSHLPAGKQ--VEI---------SLVN---------GAKNLVV--SGPPQSLYGLNLTL 393
Query: 458 KRVKGAKSTDYSDGLMYTFAENPPRSDMDFGRCP-------SYQYEGVDLLIER 504
++ K D S F+E + F P DL+ +
Sbjct: 394 RKAKAPSGLDQSR---IPFSERKLKFSNRF--LPVASPFHSHLLVPASDLINKD 442
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 35.2 bits (80), Expect = 0.038
Identities = 66/304 (21%), Positives = 100/304 (32%), Gaps = 95/304 (31%)
Query: 265 FHEGIIARYGLDSDVTRVEVCGQFPQQDI--------------------DSFIPLNIIEE 304
+++ I A+YG V Q +QD+ D+ IP I E
Sbjct: 518 YYQSIYAKYGAKGSTLIVVPFNQGSKQDVEALIEFIYDTEKNGGLGWDLDAIIPFAAIPE 577
Query: 305 A---LNREPCPDPYAPLI--------MGCDIAEEG--GDNT---VVVLRRGPVIEH---- 344
L +A I MGC ++ G T V+L P H
Sbjct: 578 QGIELEHIDSKSEFAHRIMLTNILRMMGCVKKQKSARGIETRPAQVILPMSP--NHGTFG 635
Query: 345 ---LFDWSKTDLRTTNNK-----------ISGLVEKYRPDAIIIDANN--------TGAR 382
++ SK L T N+ + G + + ++ ANN G R
Sbjct: 636 GDGMYSESKLSLETLFNRWHSESWANQLTVCGAIIGWTRGTGLMSANNIIAEGIEKMGVR 695
Query: 383 TCDYLEMLGYHVYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFASLINHSGLIQNLKSL 442
T EM + +LG +E C+ MAD +N G +Q + L
Sbjct: 696 TFSQKEM----AFNLLGLLTPEVVELCQKSPV-----MAD-------LN--GGLQFVPEL 737
Query: 443 KSFIVPNTGELAIESKRVKGAKSTDY----------SDGLMYTFAENPPRSD--MDFGRC 490
K F EL +E+ V+ A S + S Y E PR++ +DF
Sbjct: 738 KEFTAKLRKEL-VETSEVRKAVSIETALEHKVVNGNSADAAYAQVEIQPRANIQLDFPEL 796
Query: 491 PSYQ 494
Y+
Sbjct: 797 KPYK 800
>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia
coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E*
1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*
Length = 334
Score = 31.1 bits (69), Expect = 0.64
Identities = 15/119 (12%), Positives = 31/119 (26%), Gaps = 3/119 (2%)
Query: 82 ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWF 141
I A G+G L L +L+ +P C QL L+ K+
Sbjct: 29 IQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTL 88
Query: 142 ---EMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIIN 197
++ ++ + + T + + + +A
Sbjct: 89 GVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATRE 147
>2qo3_A Eryaii erythromycin polyketide synthase modules 3 and 4;
ketosynthase, acyltransferase, phosphopantetheine; 2.59A
{Saccharopolyspora erythraea}
Length = 915
Score = 30.5 bits (68), Expect = 0.84
Identities = 24/123 (19%), Positives = 36/123 (29%), Gaps = 20/123 (16%)
Query: 289 PQQDID-SFIPLNIIEEALNREPCPDPYAPLIMGCDIAEEGGDNTVVVLRRGPVIEH--- 344
P +D S + ++ +P G N V++ P EH
Sbjct: 383 PTPHVDWSSGGVALLAGN---QPWRRGERTRRAAVSAFGISGTNAHVIVEEAPEREHRET 439
Query: 345 -----------LFDWSKTDLRTTNNKISGLVEKYRPDAIIIDANNTGARTCDYLEMLGYH 393
+ S LR +I+ L+E RPDA + A T E
Sbjct: 440 TAHDGRPVPLVVSARSTAALRAQAAQIAELLE--RPDADLAGVGLGLATTRARHEHRAAV 497
Query: 394 VYR 396
V
Sbjct: 498 VAS 500
>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein
COOC; Zn-bound dimer, nickel binding protein, ATPase;
1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A*
3kje_A 3kji_A*
Length = 254
Score = 30.7 bits (68), Expect = 0.86
Identities = 32/262 (12%), Positives = 75/262 (28%), Gaps = 32/262 (12%)
Query: 81 AISAGRGIGKTTLNAWLVLWLMSTRPGISVICL-ANSETQLKTTLWAEVSKWLSLLPNKH 139
A++ G+GKTT+ A L+ + + + + ++ L TL + + ++ P
Sbjct: 4 AVAGKGGVGKTTVAAGLIKIM--ASDYDKIYAVDGDPDSCLGQTLGLSIEEAYAITPLIE 61
Query: 140 WFE------MQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGM 193
+ L P L + ++ N++
Sbjct: 62 MKDEIREKTGDGGLLILNPKVDGDLDKYGRYIDDKIFLIRMGEIKKGGSQCYCRENSFLG 121
Query: 194 AIINDEASGTPDVINLGILGFLTERNANRF-----WIMTSNPRRLSGKFYEIFNKPLDDW 248
++++ + + + + + I P S +
Sbjct: 122 SVVSALFLDKKEAVVMDMGAGIEHLTRGTAKAVDMMIAVIEPNLNS----------IKTG 171
Query: 249 KRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSFIPLN--IIEEAL 306
+ + + +I + + + P+ I IP N IE +L
Sbjct: 172 LNIE---KLAGDLGIKKVRYVINKV--RNIKEEKLIKKHLPEDKILGIIPYNELFIELSL 226
Query: 307 NREPCPDPYAPLIMG-CDIAEE 327
E P + DI ++
Sbjct: 227 KGEEIWQSTNPAFVNLHDIYQK 248
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.7 bits (63), Expect = 2.9
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 18/50 (36%)
Query: 341 VIEHLFDW---SKTDLRTTNNKISGLVEK------------Y-RPDAIII 374
V+E +W +K DL N + S VEK Y +PDA II
Sbjct: 107 VMEQ--EWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDADII 154
>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG
ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1
c.37.1.20
Length = 323
Score = 28.8 bits (63), Expect = 3.2
Identities = 17/108 (15%), Positives = 33/108 (30%)
Query: 86 RGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHWFEMQS 145
GIGKTT L L+ V+ L S+ + + ++ + + + +
Sbjct: 51 PGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKI 110
Query: 146 LSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGM 193
+ L A + +L + YS R +
Sbjct: 111 VILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQC 158
>1oju_A MDH, malate dehydrogenase; hyperthermophilic, oxidoreductase; HET:
ENA; 2.79A {Archaeoglobus fulgidus} SCOP: c.2.1.5
d.162.1.1 PDB: 1ojs_A* 2x0i_A* 2x0j_A*
Length = 294
Score = 28.5 bits (63), Expect = 3.6
Identities = 22/126 (17%), Positives = 42/126 (33%), Gaps = 10/126 (7%)
Query: 314 PYAPLIMGCDIAEEGGDNTVVVLRRGPVIEHLFDWSKTDLRTTNNKI----SGLVEKYRP 369
P I+G + ++V+ G + ++ DL N I + + + P
Sbjct: 53 DKYPKIVGGADYSLLKGSEIIVVTAGLARKP--GMTRLDLAHKNAGIIKDIAKKIVENAP 110
Query: 370 DAIIIDANNTGARTCDYLEML-GYHVYRVLGQKRAVDLEFCRNRRTELHVKMADWLEFAS 428
++ I+ N + G V G L+ R + L+ A + A
Sbjct: 111 ESKILVVTNPMDVMTYIMWKESGKPRNEVFGM--GNQLDSQR-LKERLYNAGARNIRRAW 167
Query: 429 LINHSG 434
+I G
Sbjct: 168 IIGEHG 173
>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic
region; yeast protein, ATP binding protein; 2.25A
{Saccharomyces cerevisiae} SCOP: c.37.1.6
Length = 290
Score = 28.5 bits (63), Expect = 3.6
Identities = 11/54 (20%), Positives = 17/54 (31%)
Query: 60 EVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL 113
E +D + N S +G GK+ + + LM G I
Sbjct: 14 EFLDKYIPEWFETGNKCPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGY 67
>3ddj_A CBS domain-containing protein; NP_344512.1, structural genomics,
joint center for structural genomics, JCSG; HET: AMP;
1.80A {Sulfolobus solfataricus} SCOP: d.37.1.1 d.37.1.1
Length = 296
Score = 28.3 bits (62), Expect = 4.3
Identities = 18/99 (18%), Positives = 27/99 (27%), Gaps = 5/99 (5%)
Query: 193 MAIINDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIFNKPLDDWKRFQ 252
IN+ G V N I G LT R+ G Y I P+ D
Sbjct: 43 FKKINEGGIGRIIVANEKIEGLLTTRDLLSTVESYCKDSCSQGDLYHISTTPIID----- 97
Query: 253 IDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQ 291
T + + E + + + V +
Sbjct: 98 YMTPNPVTVYNTSDEFTAINIMVTRNFGSLPVVDINDKP 136
>1c8b_A Spore protease; novel fold; 3.00A {Bacillus megaterium} SCOP:
c.56.1.2
Length = 371
Score = 28.3 bits (63), Expect = 4.9
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 360 ISGLVEKYRPDAII-IDA 376
I G+V+K PD II IDA
Sbjct: 178 IFGVVKKVNPDFIIAIDA 195
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
e.8.1.1
Length = 847
Score = 28.0 bits (61), Expect = 5.1
Identities = 26/159 (16%), Positives = 44/159 (27%), Gaps = 25/159 (15%)
Query: 225 IMTSNP---RRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGI------------ 269
I+ +P RRL + + + + + D + G+ G
Sbjct: 98 IVVRDPLAVRRLRNDVPKAYEAHIKYFNNYMYDIGLIPGMPYVVKNGKLESVYLSLDEKD 157
Query: 270 ---IARYGLDSDVTRVEVCGQFPQQDIDSFIPLNI----IE---EALNREPCPDPYAPLI 319
I + DSD ++ + + IE R P I
Sbjct: 158 VEEIKKAFADSDEMTRQMAVDWLPIFETEIPKIKRVAIDIEVYTPVKGRIPDSQKAEFPI 217
Query: 320 MGCDIAEEGGDNTVVVLRRGPVIEHLFDWSKTDLRTTNN 358
+ +A G V+VL R V E + N
Sbjct: 218 ISIALAGSDGLKKVLVLNRNDVNEGSVKLDGISVERFNT 256
>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus
abyssi}
Length = 350
Score = 28.0 bits (60), Expect = 5.8
Identities = 25/198 (12%), Positives = 45/198 (22%), Gaps = 6/198 (3%)
Query: 81 AISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKHW 140
+ R +GK++L L A + L E+ +S
Sbjct: 35 LLLGIRRVGKSSL-LRAFLNERPGILIDCRELYAERGHITREELIKELQSTISPFQKFQS 93
Query: 141 FEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFV-----GHHNTYGMAI 195
SL+L L + D G +
Sbjct: 94 KFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGSRGGKELLA 153
Query: 196 INDEASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYEIFNKPLDDWKRFQIDT 255
+ A + + + + G + I E+ KP D +
Sbjct: 154 LFAYAYDSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLK 213
Query: 256 RTVEGIDPSFHEGIIARY 273
R ++ E I
Sbjct: 214 RGFREVNLDVPENEIEEA 231
>2ck3_D ATP synthase beta chain; ATP phosphorylase, ATP phosphorylase (H+
transporting), F1FO ATP synthase, F1-ATPase, hydrolase,
ATP synthesis; HET: ANP ADP; 1.9A {Bos taurus} SCOP:
a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D*
1e1r_D* 1efr_D* 1e79_E* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D*
1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D*
2w6j_D 2w6e_D 2w6g_D ...
Length = 482
Score = 27.5 bits (61), Expect = 6.9
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 79 KGAISAGRGIGKTTLNAWLVLWLMSTRPGISVICL 113
K + G G+GKT L L+ + G SV
Sbjct: 155 KIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAG 189
>3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M
3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M
2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ...
Length = 118
Score = 27.5 bits (61), Expect = 7.5
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 240 IFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSF--- 296
I + D K I ++ G+ + + I+A G+ DV + + ID+
Sbjct: 4 IAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVK----ISELSEGQIDTLRDE 59
Query: 297 IPLNIIEEALNRE 309
+ ++E L RE
Sbjct: 60 VAKFVVEGDLRRE 72
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
0.320 0.137 0.431
Gapped
Lambda K H
0.267 0.0450 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 4,713,737
Number of extensions: 222983
Number of successful extensions: 734
Number of sequences better than 10.0: 1
Number of HSP's gapped: 734
Number of HSP's successfully gapped: 24
Length of query: 511
Length of database: 5,693,230
Length adjustment: 97
Effective length of query: 414
Effective length of database: 3,341,562
Effective search space: 1383406668
Effective search space used: 1383406668
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 (21.8 bits)
S2: 59 (27.2 bits)