RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780454|ref|YP_003064867.1| DNA polymerase III subunit
beta [Candidatus Liberibacter asiaticus str. psy62]
(385 letters)
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp,
DNA replication, rational drug design, antibiotic
target, transferase; HET: DNA 322; 1.64A {Escherichia
coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A*
1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 1jql_A*
1jqj_A* 3f1v_A*
Length = 366
Score = 216 bits (550), Expect = 8e-57
Identities = 128/386 (33%), Positives = 212/386 (54%), Gaps = 21/386 (5%)
Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIP-A 59
MK TVER +L+ L + + T+P+ ++LLQ DG L + + E+E+ +
Sbjct: 1 MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV 60
Query: 60 SVDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
G+ TV A +DI R L +GA+I+ E E + + G S F L + P ++FP
Sbjct: 61 QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGE---RMLVRSGRSRFSLSTLPAADFP 117
Query: 120 STKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGH 179
+ + + F L + +K L+E T F+MA +++RYYLNG+ F E+L+ A TDGH
Sbjct: 118 NLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVA--TDGH 175
Query: 180 RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIESLSMSV 239
RLAV + I + S+IVPRK V E++R+L D+ ++V + + I ++ +
Sbjct: 176 RLAVCSMPIGQSL-PSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTS 234
Query: 240 RLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMTV 299
+L+DG FP+Y+ V+P + DK L C L+QA R +I+S+ + + V+L +S ++L +T
Sbjct: 235 KLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITA 294
Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFI 359
+NP+ +A E ++V Y+ M+I FN Y+L++++ + + V L S SSV I
Sbjct: 295 NNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKC-----ENVRMMLTDSVSSVQI 349
Query: 360 RGKDKDSKNNKDNKVNAFYVLMPMRI 385
+A YV+MPMR+
Sbjct: 350 EDAASQ---------SAAYVVMPMRL 366
>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomics,
joint center for structural genomics, JCSG, protein
structure initiative; HET: DNA; 2.00A {Thermotoga
maritima MSB8} SCOP: d.131.1.1 d.131.1.1 d.131.1.1
Length = 378
Score = 198 bits (504), Expect = 2e-51
Identities = 94/387 (24%), Positives = 186/387 (48%), Gaps = 24/387 (6%)
Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
MK+TV ++ + + A + + +K+ P+ L + DG I A+ E + + A+
Sbjct: 13 MKVTVTTLELKDKITIASKALAKKSVKPILAGFLFEVKDGNFYICATDLETGVKATVNAA 72
Query: 61 -VDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFP 119
+ V ++ +V+ L D + + L IS G + F + + P EFP
Sbjct: 73 EISGEARFVVPGDVIQKMVKVLPDEITELSLEGDAL----VISSGSTVFRITTMPADEFP 128
Query: 120 STKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGH 179
E +FE+ +S+L+ +VE+ FA A +E LNG+F+ +++ L+L A +DG
Sbjct: 129 EITPAESGITFEVDTSLLEEMVEKVIFAAAKDEFMRNLNGVFWELHKNLLRLVA--SDGF 186
Query: 180 RLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKV-SLSESRIHLNIESLSMS 238
RLA+AE I + S ++ K++ E+ +L + R+ L+ +
Sbjct: 187 RLALAEEQIENEE--EASFLLSLKSMKEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETV 244
Query: 239 VRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSVRIQAVKLSLSSDKLCMT 298
+R++D EFP+Y+ VIP + ++ V+ LR+++ RV +++S ++VK + + + +
Sbjct: 245 MRVVDAEFPDYKRVIPETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLV 304
Query: 299 VDNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVF 358
+PD G+ ++ + V + I FN K++ +++ +I + +E+ S S
Sbjct: 305 SKSPDYGEVVDEVEVQKEGEDLVIAFNPKFIEDVLKHIET-----EEIEMNFVDSTSPCQ 359
Query: 359 IRGKDKDSKNNKDNKVNAFYVLMPMRI 385
I D Y++MP+R+
Sbjct: 360 INPLDIS---------GYLYIVMPIRL 377
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp,
replication, transferase; HET: DNA; 2.00A {Streptococcus
pyogenes} PDB: 2awa_A*
Length = 378
Score = 175 bits (443), Expect = 2e-44
Identities = 80/394 (20%), Positives = 166/394 (42%), Gaps = 27/394 (6%)
Query: 1 MKITVERSDILELLGHACRIIERKNTIPVSCHVLLQANDGLLEIKASGPEIEITGAIPAS 60
++ ++ R+ + L R I KN IP+ + ++ + + S +I I IP S
Sbjct: 2 IQFSINRTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIPVS 61
Query: 61 -------VDVCGSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSF 113
+ G+I + A +I+ L D + E ++ G S L+
Sbjct: 62 NENAGLLITSPGAILLEASFFINIISSLPDISINVKEIEQHQVV---LTSGKSEITLKGK 118
Query: 114 PESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCA 173
++P +E L + +LK+++ T FA + +E R L G+ ++ K
Sbjct: 119 DVDQYPRLQEVSTENPLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNH--KDFK 176
Query: 174 VATDGHRLAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSSKDSSVKVSLSESRIHLNIE 233
+ + + +++P K++ E + + +V+V S S+I E
Sbjct: 177 AVATDSHRMSQRLITLDNTSADFMVVLPSKSLREFSAVFTDDIETVEVFFSPSQILFRSE 236
Query: 234 SLSMSVRLIDGEFPNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMSSV-RIQAVKLSLSS 292
+S RL++G +P+ ++ + E+ N +LR A++R ++S+ + VKL ++
Sbjct: 237 HISFYTRLLEGNYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQ 296
Query: 293 DKLCMTVDNPDMGKAIESMN-VYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLD 351
+ + V++P++GK E ++ V + + I FN YL+E + I S + V
Sbjct: 297 NHISAHVNSPEVGKVNEDLDIVSQSGSDLTISFNPTYLIESLKAIKS-----ETVKIHFL 351
Query: 352 SSNSSVFIRGKDKDSKNNKDNKVNAFYVLMPMRI 385
S + D++ + ++ P+R
Sbjct: 352 SPVRPFTLTPGDEEE--------SFIQLITPVRT 377
>3k4x_A PCNA, proliferating cell nuclear antigen; DNA replication,
DNA-binding; HET: DNA; 2.98A {Saccharomyces cerevisiae}
Length = 798
Score = 75.5 bits (186), Expect = 2e-14
Identities = 39/223 (17%), Positives = 85/223 (38%), Gaps = 23/223 (10%)
Query: 140 LVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRLAVAEVDIVA------QIA 193
E + F + + + + F E+ + A D R+ + ++I +
Sbjct: 12 FEEASLFKRIIDGFKDCVQLVNFQCKEDGIIA--QAVDDSRVLLVSLEIGVEAFQEYRCD 69
Query: 194 KMPSIIVPRKAVGEILRILSSKDS-SVKVSLSESRIHLNIES------LSMSVRLIDGEF 246
++ + ++ +ILR ++ D+ ++ + I L E S++L+D +
Sbjct: 70 HPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDA 129
Query: 247 PNYQNVIPCSNDKELRVNCTNLRQAVDRVSIMS-SVRIQA----VKLSLSSD--KLCMTV 299
+ + D L + + + V +S +S S+ I +K D + +
Sbjct: 130 DFLK-IEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVII 188
Query: 300 DNPDMGKAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVV 342
+ E+ + P+D+ F KYLL+II S + V
Sbjct: 189 KPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRV 231
>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 = 48.4 bits (115), Expect = 3e-06
Identities = 66/409 (16%), Positives = 125/409 (30%), Gaps = 183/409 (44%)
Query: 26 TIPVSCHVLLQANDGLLEI-------KASG--P-EIE-----ITG---------AIPASV 61
+IP+SC ++ G++++ K G P E+ TG AI A
Sbjct: 233 SIPISCPLI-----GVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAI-AET 286
Query: 62 DVCGSITVSAHLLYDIVRKLQDGA-QISFFKENELGTEVNISHGDSNFYLQSFPESEFPS 120
D S + VRK A + FF +G + +++P +
Sbjct: 287 DSWES-------FFVSVRK----AITVLFF----IGVR---CY-------EAYPNT---- 317
Query: 121 TKEEEYVYSFELASSVLKNLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHR 180
L S+L++ +E N E
Sbjct: 318 ----------SLPPSILEDSLE---------------NN------E--------GVPSPM 338
Query: 181 LAVAEVDIVAQIAKMPSIIVPRKAVGEILRILSS---KDSSVKVSLSESRIHLNI----E 233
L+++ ++ ++ V + + +S V++SL +L + +
Sbjct: 339 LSIS--NL------------TQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQ 384
Query: 234 SL-SMSVRL--------IDGEFPNYQNVIPCSNDKELRVNCTN-------------LRQA 271
SL +++ L +D Q+ IP S K + +N L A
Sbjct: 385 SLYGLNLTLRKAKAPSGLD------QSRIPFSERK---LKFSNRFLPVASPFHSHLLVPA 435
Query: 272 VDRVSIMSSVRIQAVKLSLSSDKLCM----TVDNPDMGKAIESMNVYYNECPMDICFNYK 327
D + + + +S ++ + + T D D+ S
Sbjct: 436 SDLI----NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGS----------------- 474
Query: 328 YLLE-IIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKD----SKNNKD 371
+ E I+D I V E + +++ F G + NKD
Sbjct: 475 -ISERIVDCIIR-LPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKD 521
Score = 38.4 bits (89), Expect = 0.003
Identities = 45/266 (16%), Positives = 83/266 (31%), Gaps = 83/266 (31%)
Query: 65 GSITVSAHLLYDIVRKLQDGAQISFFKENELGTEVNISHGDSNFYLQSFPESEFPSTKEE 124
GS+ + SFF ++L + F + PE ++
Sbjct: 14 GSLEHVLLVPTA-----------SFFIASQLQEQ---------F-NKILPEPTEGFAADD 52
Query: 125 EYVYSFELASSVLK---NLVERTHFAMATEEIRYYLNGIFFHINEEDLKLCAVATDGHRL 181
E EL L +LVE + + + L F E L D H L
Sbjct: 53 EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLT--EF---ENCY-LE--GNDIHAL 104
Query: 182 AVAEVDIVAQIAKMPSII-VPRKAVGEILR-----ILSSKDSSVKVSLSESRIHLNIESL 235
A AK+ E+++ + +K K S S +L
Sbjct: 105 A----------AKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS---------AL 145
Query: 236 SMSVRLIDGEFPNY-----QNVIPCSND--KELR-VNCT---NLRQAVDRVSIMSSVRIQ 284
+V +G Q ++D +ELR + T + D + + +
Sbjct: 146 FRAVG--EGNAQLVAIFGGQG---NTDDYFEELRDLYQTYHVLVG---DLIKFSAETLSE 197
Query: 285 AVKLSLSSDKLC---MTV----DNPD 303
++ +L ++K+ + + +NP
Sbjct: 198 LIRTTLDAEKVFTQGLNILEWLENPS 223
Score = 30.7 bits (69), Expect = 0.57
Identities = 37/166 (22%), Positives = 73/166 (43%), Gaps = 23/166 (13%)
Query: 41 LLEIKASGPEIEITGAIPASVDVCG-SITVSAHL--LYDIVRKLQDGAQISFFKENELGT 97
L+E KA+ +++ G IPA G S+ A L L D++ ++ ++ F++ +
Sbjct: 1738 LME-KAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM-SIESLVEVVFYR--GMTM 1793
Query: 98 EVNISH---GDSNFYLQSF-PESEFPSTKEEEYVYSFELASSVLKNLVERTHFAMATEEI 153
+V + G SN+ + + P S +E Y E LVE ++ + E
Sbjct: 1794 QVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNV--ENQ 1851
Query: 154 RYYLNGIFFHINEEDLKLCAVATDG-HRLAVAEVDIVAQIAKMPSI 198
+Y G DL+ T+ + + + ++DI+ ++ K S+
Sbjct: 1852 QYVAAG--------DLRALDTVTNVLNFIKLQKIDII-ELQKSLSL 1888
>1v1p_B Exotoxin 1; virulence factor, antigen presenting cell, secreted
protein, SET1, superantigen, OB-fold, {beta}-grAsp; 2.7A
{Staphylococcus aureus} SCOP: b.40.2.2 d.15.6.1 PDB:
1v1o_A 1v1p_A 2qej_C*
Length = 213
Score = 27.9 bits (62), Expect = 3.7
Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 8/74 (10%)
Query: 306 KAIESMNVYYNECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKD 365
I ++ YY+ + + + + V F N +F+ GKDK+
Sbjct: 23 HDIRDLHRYYSSESFE--------YSNVSGKVENYNGSNVVRFNPKDQNHQLFLLGKDKE 74
Query: 366 SKNNKDNKVNAFYV 379
N F V
Sbjct: 75 QYKEGLQGQNVFVV 88
>3jrs_A PYL1, putative uncharacterized protein AT5G46790; plant hormone
receptor, abscisic acid; HET: A8S; 2.05A {Arabidopsis
thaliana}
Length = 208
Score = 27.2 bits (60), Expect = 7.0
Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 2/47 (4%)
Query: 209 LRILSSKDSSVKVSLSESRIHLNIESLSMSVRLIDGEFP--NYQNVI 253
R ++ + E L+ + + GE NY++V
Sbjct: 102 TRDVNVISGLPANTSRERLDLLDDDRRVTGFSITGGEHRLRNYKSVT 148
>3g65_A Cell cycle checkpoint control protein RAD9A; PCNA, DNA binding
clamp, DNA damage, DNA repair, exonuclease, hydrolase,
nuclease, nucleus, phosphoprotein; 2.90A {Homo sapiens}
Length = 296
Score = 26.8 bits (59), Expect = 8.5
Identities = 24/184 (13%), Positives = 57/184 (30%), Gaps = 18/184 (9%)
Query: 203 KAVGEILRILSSKDSSVKVSLSESRIHL----NIESLSMSVRLIDGEFPNYQNVIPCSND 258
K +G+ + LS + + E + L + S F YQ P +
Sbjct: 11 KVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDL 70
Query: 259 KELRVNCTNLRQAVDRV-SIMSSVRIQAVKLSLSSDKLCMTVDNPDMGK--------AIE 309
++ + + + +V + L+ S +L + + + E
Sbjct: 71 LRCKILMKSFLSVFRSLAMLEKTVEKCCISLNGRSSRLVVQLHCKFGVRKTHNLSFQDCE 130
Query: 310 SMNVYYN--ECPMDICFNYKYLLEIIDNISSDEVVDDEVVFRLDSSNSSVFIRGKDKDSK 367
S+ ++ CP + + L E + S EV + + ++++
Sbjct: 131 SLQAVFDPASCPHMLRAPARVLGEAVLPFSP---ALAEVTLGIGRGRRVILRSYHEEEAD 187
Query: 368 NNKD 371
+
Sbjct: 188 STAK 191
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
0.318 0.134 0.374
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,192,172
Number of extensions: 146348
Number of successful extensions: 375
Number of sequences better than 10.0: 1
Number of HSP's gapped: 365
Number of HSP's successfully gapped: 15
Length of query: 385
Length of database: 5,693,230
Length adjustment: 94
Effective length of query: 291
Effective length of database: 3,414,294
Effective search space: 993559554
Effective search space used: 993559554
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 (21.7 bits)
S2: 58 (26.2 bits)