RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780874|ref|YP_003065287.1| peptide chain release factor 1 [Candidatus Liberibacter asiaticus str. psy62] (357 letters) >gnl|CDD|30565 COG0216, PrfA, Protein chain release factor A [Translation, ribosomal structure and biogenesis]. Length = 363 Score = 466 bits (1201), Expect = e-132 Identities = 203/357 (56%), Positives = 274/357 (76%), Gaps = 7/357 (1%) Query: 7 KQICDLKNRFAEIELRMSE---SPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLH 63 +++ L R+ E+E +S+ D Y KL++EYA + PI+ K Y + +++ +D Sbjct: 7 EKLESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAK 66 Query: 64 TVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGS 123 ++ + D E+R++A+ E+ +E +I ELE E+ LLLPKD +DDK+ ILEIRAGTGG Sbjct: 67 EMLAE-EKDPEMREMAEEEIKELEAKIEELEEELKILLLPKDPNDDKNIILEIRAGTGGD 125 Query: 124 EAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVH 183 EAALF GDLFRMY RYA + WKVE+LS+S+++ GGYKEI+A+ISG+GV+SR+KFESGVH Sbjct: 126 EAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKFESGVH 185 Query: 184 RVQRVPATEASGRVHTSAATVAVLPEAAEI-DVDIPLEDIRIDTMRASGSGGQHVNTTDS 242 RVQRVPATE+ GR+HTSAATVAVLPE E+ +++I +D+RIDT R+SG+GGQHVNTTDS Sbjct: 186 RVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDS 245 Query: 243 AVRITHIPTGIMVTSS-EKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGD 301 AVRITH+PTGI+V E+SQH+N+ +AMKVLRARLYD ER++ E ++ RK Q+GSGD Sbjct: 246 AVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASERKSQVGSGD 305 Query: 302 RSERIRTYNFSQGRITDHRINLTLYKLEYVLQGY-IDDIINPLLTAHQAKMIGSASE 357 RSERIRTYNF Q R+TDHRINLTLYKL+ V++G +D+II+ L+ QA+ + E Sbjct: 306 RSERIRTYNFPQNRVTDHRINLTLYKLDEVMEGGKLDEIIDALIAEDQAEQLAELGE 362 >gnl|CDD|37937 KOG2726, KOG2726, KOG2726, Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis]. Length = 386 Score = 302 bits (775), Expect = 8e-83 Identities = 142/322 (44%), Positives = 200/322 (62%), Gaps = 5/322 (1%) Query: 41 AISPIISKISIYDQKKQEEQDLHT--VIGDHNSDSEIRDLAQIEVLAIEKEIRELENEIN 98 + + ++ + + ++L + + D ++ +LA+ E I KEI +E+ Sbjct: 65 DPAELDEVLNALSDRMKLVRELKSLKSLIKEGEDEDMDELAEEEAEEISKEIERSLHELE 124 Query: 99 YLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDG 158 LLP D D ++CI+E+RAG GG EA +F +L MY++YA WK VL + + G Sbjct: 125 LSLLPSDPYDAEACIIEVRAGAGGQEAQIFTMELVDMYQKYAERLGWKARVLEKAPGESG 184 Query: 159 GYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPE--AAEIDVD 216 G K I G + +KFE+GVHRVQRVP+TE SGR HTS A+VAV+P+ E+DV+ Sbjct: 185 GIKSATLEIEGESAYGYLKFEAGVHRVQRVPSTETSGRRHTSTASVAVIPQPGRDEVDVE 244 Query: 217 IPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSS-EKSQHQNRLRAMKVLRA 275 I +D+RI+T RASG GGQHVN TDSAVR+THIPTGI+V E+SQH+NR A+K LRA Sbjct: 245 IDEKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALKRLRA 304 Query: 276 RLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGY 335 +L + R+ + E RK Q+GS RSE+IRTYNF Q R+TDHRI L + LE L G Sbjct: 305 KLAVIYREEKSEEEKKKRKAQVGSLKRSEKIRTYNFKQDRVTDHRIGLESHDLESFLDGN 364 Query: 336 IDDIINPLLTAHQAKMIGSASE 357 +D++I LL+ + + + E Sbjct: 365 LDELIEALLSLRREEDLAELLE 386 >gnl|CDD|31379 COG1186, PrfB, Protein chain release factor B [Translation, ribosomal structure and biogenesis]. Length = 239 Score = 191 bits (487), Expect = 2e-49 Identities = 99/236 (41%), Positives = 143/236 (60%), Gaps = 4/236 (1%) Query: 112 CILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRG 171 L I AG GG+EA + L RMY R+A + +KVEVL +SD ++ G K I G Sbjct: 1 AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60 Query: 172 VFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAE-IDVDIPLEDIRIDTMRAS 230 + +K E+GVHR+ R+ +++GR HTS A+V V PE I+++IP +D+RIDT RAS Sbjct: 61 AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRAS 120 Query: 231 GSGGQHVNTTDSAVRITHIPTGIMVTS-SEKSQHQNRLRAMKVLRARLYDVERKRMANER 289 G+GGQHVN TDSAVR+TH+PTGI+V +E+SQH N+ A K+L+ +LY + +++ + E+ Sbjct: 121 GAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQEK 180 Query: 290 SANRKLQIGSGDRSERIRTYNFSQGRIT-DHRINLTLYKLEYVLQGYIDDIINPLL 344 + R L+ G +IR+Y + T D R + VL G D I L Sbjct: 181 NRERALKKLIG-WGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGDKDGFIKAYL 235 >gnl|CDD|144168 pfam00472, RF-1, RF-1 domain. This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis. Length = 114 Score = 170 bits (433), Expect = 5e-43 Identities = 61/114 (53%), Positives = 85/114 (74%), Gaps = 1/114 (0%) Query: 208 PEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSS-EKSQHQNR 266 P E++++IP D+RIDT R+SG GGQ+VN T+SAVR+TH+PTGI+V E+SQH+NR Sbjct: 1 PLDEEVEIEIPPSDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNR 60 Query: 267 LRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHR 320 +A++ L+A+LY+ E ++ E RK Q+ GDR E+IRTYNF QGR+ DHR Sbjct: 61 EKALERLKAKLYEAELQKKREETKPTRKSQVRRGDRKEKIRTYNFPQGRVKDHR 114 >gnl|CDD|146218 pfam03462, PCRF, PCRF domain. This domain is found in peptide chain release factors. Length = 115 Score = 155 bits (395), Expect = 1e-38 Identities = 59/109 (54%), Positives = 75/109 (68%) Query: 71 SDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVG 130 D E+R+LA+ E+ +EKE+ ELE E+ LLLP D DDK+ ILEIRAG GG+EA LF Sbjct: 7 DDPELRELAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQLFAE 66 Query: 131 DLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFE 179 DL RMY+RYA + WKVEVL S+ ++GG KE I G G + +KFE Sbjct: 67 DLLRMYQRYAERKGWKVEVLDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115 >gnl|CDD|38639 KOG3429, KOG3429, KOG3429, Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]. Length = 172 Score = 35.4 bits (81), Expect = 0.022 Identities = 26/126 (20%), Positives = 47/126 (37%), Gaps = 39/126 (30%) Query: 210 AAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAV------------------------- 244 A IPL+ + I R+SG GGQ+VN ++ V Sbjct: 30 AIHFKGKIPLDQLEISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEK 89 Query: 245 -RITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLY-------------DVERKRMANERS 290 RI ++ + +SQH+N ++ LR + +++ R+ E++ Sbjct: 90 NRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAAEQTPPVDPTEETIKKIRIRKEKA 149 Query: 291 ANRKLQ 296 +LQ Sbjct: 150 NRERLQ 155 >gnl|CDD|35429 KOG0208, KOG0208, KOG0208, Cation transport ATPase [Inorganic ion transport and metabolism]. Length = 1140 Score = 30.7 bits (69), Expect = 0.66 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 5/54 (9%) Query: 38 EYAAISPIISKISI----YDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIE 87 YA IIS SI Y+ +KQ L +++ + IRD V + E Sbjct: 215 YYAFCIVIISVYSIVLSVYETRKQS-IRLRSMVKFTCPVTVIRDGFWETVDSSE 267 >gnl|CDD|144201 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A. Length = 428 Score = 30.2 bits (69), Expect = 0.88 Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%) Query: 75 IRDLAQIEVLAIEKEIRELENEINYL--LLPKDTD 107 +R L + E+ +EKEI ELE EI L +L + Sbjct: 387 LRRLTKEEIEKLEKEIEELEKEIAELEKILASEKK 421 >gnl|CDD|38824 KOG3618, KOG3618, KOG3618, Adenylyl cyclase [General function prediction only]. Length = 1318 Score = 30.0 bits (67), Expect = 1.0 Identities = 32/157 (20%), Positives = 55/157 (35%), Gaps = 32/157 (20%) Query: 175 RMKFESGVHRVQRVPATEASG---RVHTSAATVAVLPEAAEI----DVDIPLEDIRIDTM 227 R KF+ + V E+SG +VH S AT L + E+ ++ + + + Sbjct: 452 RFKFDVWSNDVNLANLMESSGVAGKVHISEATAKYLDDRYEMEEGKVIEGLGQSVVAGQL 511 Query: 228 RASGSG--------GQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYD 279 R + G GQ + + S + N ++ K R D Sbjct: 512 RRTNPGTLKTYLISGQRGASAKES-----------RCSVAEVLSLNSMKMRKKSSGRDRD 560 Query: 280 VERKRMANERSANRKLQI--GSG----DRSERIRTYN 310 E + S + Q SG +ER+RT++ Sbjct: 561 FEVIDGSQVSSIPPRGQGRESSGSLKIKLAERVRTFD 597 >gnl|CDD|32549 COG2414, COG2414, Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]. Length = 614 Score = 29.1 bits (65), Expect = 1.8 Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 1/70 (1%) Query: 77 DLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMY 136 ++ ++L + I LE N K DD + GG A DL M Sbjct: 526 EMTPEDLLKAGERIYNLERAYNVKAGVKPEDDTLPKRVFEEPLPGGP-AKGDRNDLEEML 584 Query: 137 ERYAALRKWK 146 E Y LR W Sbjct: 585 EEYYKLRGWD 594 >gnl|CDD|31718 COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large subunit CoxL/CutL homologs [Energy production and conversion]. Length = 731 Score = 28.8 bits (64), Expect = 2.6 Identities = 22/122 (18%), Positives = 42/122 (34%), Gaps = 5/122 (4%) Query: 119 GTGGSEAALFVGDLFRMYERYAALR-KWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMK 177 G+ GS G A + + +D +D ++ + G S + Sbjct: 503 GSVGSRGTAVAGSAVIDAAAKLAEKDPVAAARMLGADAEDVVLEDGAFKVGGGDRRSAVS 562 Query: 178 FESGVHR-VQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQH 236 + + + A AS + A AE++VD ++R+ + A G+ Sbjct: 563 LKEVAGKGLAPGLAVAASFGSDNTYPYGAH---IAEVEVDPETGEVRVLRVVAVDDCGRV 619 Query: 237 VN 238 VN Sbjct: 620 VN 621 >gnl|CDD|37877 KOG2666, KOG2666, KOG2666, UDP-glucose/GDP-mannose dehydrogenase [Carbohydrate transport and metabolism, Signal transduction mechanisms]. Length = 481 Score = 28.4 bits (63), Expect = 3.3 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 7/57 (12%) Query: 4 LSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQ 60 +S K+I L F + E+P++D L E+ A ++SIYD + EEQ Sbjct: 322 VSDKKIAILGFAFKKDTGDTRETPAIDVCKGLLEDKA-------RLSIYDPQVTEEQ 371 >gnl|CDD|147274 pfam05009, EBV-NA3, Epstein-Barr virus nuclear antigen 3 (EBNA-3). This family contains EBNA-3A, -3B, and -3C which are latent infection nuclear proteins important for Epstein-Barr virus (EBV)-induced B-cell immortalisation and the immune response to EBV infection. Length = 254 Score = 27.4 bits (61), Expect = 5.9 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%) Query: 274 RARLYDVERKRMANERSANRKLQIGS-----GDRSERIRTYNFSQGRITDHRINLT 324 R R D+ R + + KL S G R+ + Y++ R+ RI LT Sbjct: 4 RQRCRDIRRGPLPIRGQRHWKLTSPSRTWPMGYRTASLWMYSYEDDRVGADRIMLT 59 >gnl|CDD|145318 pfam02092, tRNA_synt_2f, Glycyl-tRNA synthetase beta subunit. Length = 549 Score = 27.4 bits (62), Expect = 6.1 Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 18/52 (34%) Query: 271 KVLRARLYDVE-------RKRMANERSANRKL-------QIGS-GDRSERIR 307 +VLRARL D E + + S KL ++GS D+ ERI Sbjct: 315 RVLRARLADAEFFYEEDLKTPLE---SRVEKLKKVVFQEKLGSLYDKVERIE 363 >gnl|CDD|29149 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.. Length = 445 Score = 27.1 bits (60), Expect = 8.2 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 6/67 (8%) Query: 41 AISPIISKISIYDQKKQ------EEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELE 94 I +I+ I D+ K+ E+ + D D +R L ++E + KE++ELE Sbjct: 359 NIDEVINLIRSSDEAKKALIEELEKLGFSEIQADAILDMRLRRLTKLEREKLLKELKELE 418 Query: 95 NEINYLL 101 EI L Sbjct: 419 AEIEDLE 425 >gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only]. Length = 620 Score = 26.9 bits (59), Expect = 9.9 Identities = 28/160 (17%), Positives = 53/160 (33%), Gaps = 25/160 (15%) Query: 18 EIELRMSESPSVD-----AYIKLTEEYAAISPIISKISIYD----------QKKQEEQDL 62 +IE + +V+ + +Y + I+ ++ D EE++ Sbjct: 394 DIEAENGGAYNVELRDKYILQDPSWKYDIMPEILDGKNVADFVDPEIEAKLLALDEEEER 453 Query: 63 HTVIGDHNSDSEIRDLAQIEVLAIEKEIRE---------LENEINYLLLPKDTDDDKSCI 113 G ++SD EI D + EVL IRE + + N +LP+ + Sbjct: 454 LEREGYYDSDQEIEDEDEEEVLEKASRIREKNKLTMLAARQKKKNRPVLPRTAGRTLDEL 513 Query: 114 LEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSS 153 + G ++ R A +E + S Sbjct: 514 QS-SLQSLGLDSDSIEERARRAANEMADGSGVDLEEIRSK 552 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.316 0.132 0.362 Gapped Lambda K H 0.267 0.0671 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,076,939 Number of extensions: 212062 Number of successful extensions: 575 Number of sequences better than 10.0: 1 Number of HSP's gapped: 564 Number of HSP's successfully gapped: 24 Length of query: 357 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 262 Effective length of database: 4,210,882 Effective search space: 1103251084 Effective search space used: 1103251084 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)