RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781047|ref|YP_003065460.1| AFG1-family ATPase [Candidatus Liberibacter asiaticus str. psy62] (404 letters) >gnl|CDD|31674 COG1485, COG1485, Predicted ATPase [General function prediction only]. Length = 367 Score = 333 bits (856), Expect = 4e-92 Identities = 138/371 (37%), Positives = 215/371 (57%), Gaps = 17/371 (4%) Query: 6 VSSRLISLIQDKKLKYNPAQESVVKSFDRLLVDLYKQQKQEQGIFSWLWNLRGIKRKYCS 65 R L+ + +PAQ + + DRL D + + WL+ R + Sbjct: 11 PVERYAQLVPAGTFQPDPAQPAAAAALDRLY-DELVAPRSARKALGWLF-----GRDHGP 64 Query: 66 MQGIYLHGDVGQGKSMLMNLFFALVPIEKKCRLHFYEFMKDVHSRIIMYRKKIEFGEILE 125 ++G+YL G VG+GK+MLM+LF+ +P E+K RLHF+ FM VH R+ + + Sbjct: 65 VRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQG--------Q 116 Query: 126 SDPIPLVASSIALESRVLCFDEFMITNIADAIILSRLFAALFSHGCIIVMTSNFIPENLY 185 +DP+P +A +A E+RVLCFDEF +T+IADA+IL RL ALF+ G ++V TSN P+NLY Sbjct: 117 TDPLPPIADELAAETRVLCFDEFEVTDIADAMILGRLLEALFARGVVLVATSNTAPDNLY 176 Query: 186 KDEINRNVLVSFIELLEKKLEIISLDSGQDYRRKEQSILPIYMTPLNSYNRVLMDKLWAH 245 KD + R + I+L++ E++++D DYR ++ P+Y+TPL++ +DKLWA Sbjct: 177 KDGLQRERFLPAIDLIKSHFEVVNVDGPVDYRLRKLEQAPVYLTPLDAEAEAALDKLWAA 236 Query: 246 ITKGKKSLSLNISTEGGYEIHVPFFCSRVSRFSFFDLCDRPLSANDFVEIANRFDVVIIN 305 ++ G + N+ G EI VP + F F LC+ P SA+D++ +A RF V + Sbjct: 237 LSDGAPEAAANL-EIKGREIRVPAVAGGLLWFDFAQLCEAPRSASDYLALAERFHTVFLT 295 Query: 306 DIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDLFPYKLRKGAFEIQRTVSRL 365 D+P + +D +RFI L+D Y+ + L+ S+E + +L+ + AFE QRT+SRL Sbjct: 296 DVPQMDPLDRDEARRFIALVDELYDRGVKLVASAEVPLNELYQGG--RLAFEFQRTLSRL 353 Query: 366 YEMFSAQYIGK 376 EM S +Y+G Sbjct: 354 QEMQSEEYLGI 364 >gnl|CDD|112768 pfam03969, AFG1_ATPase, AFG1-like ATPase. This family of proteins contains a P-loop motif and are predicted to be ATPases. Length = 361 Score = 287 bits (735), Expect = 5e-78 Identities = 131/372 (35%), Positives = 197/372 (52%), Gaps = 19/372 (5%) Query: 8 SRLISLIQDKKLKYNPAQESVVKSFDRLLVDLYKQQKQEQ-GIFSWLWNLRGIKRKYCSM 66 R + +Q + + AQ + V + DRL L Q G LW G KR + + Sbjct: 5 QRYTAQLQRGAIFPDVAQANAVPALDRLYQRLQAADFVRQSGAGGKLW---GRKRSHQPV 61 Query: 67 QGIYLHGDVGQGKSMLMNLFFALVPIEKKCRLHFYEFMKDVHSRIIMYRKKIEFGEILES 126 +G+YL G VG+GK+ LM+ FF +P E+K R HF+ FM VH + + Sbjct: 62 RGLYLWGGVGRGKTHLMDSFFESLPGERKRRTHFHRFMFRVHDEL-TTLQG-------GD 113 Query: 127 DPIPLVASSIALESRVLCFDEFMITNIADAIILSRLFAALFSHGCIIVMTSNFIPENLYK 186 DP+P+ A A E+R+LCFDEF + +I DA+IL RLF ALF+ G +V TSN PE LY+ Sbjct: 114 DPLPIAADRFANEARLLCFDEFEVDDIGDAMILGRLFEALFARGVSLVATSNTAPEQLYR 173 Query: 187 DEINRNVLVSFIELLEKKLEIISLDSGQDYRRKEQSILPIYMTPLNSYNRVLMDKLWAHI 246 + +NR + I+LLE E++ +D DYR + P+++ PL+ +D+LW + Sbjct: 174 NGLNRQRFLPAIDLLESHFEVVRVDGPVDYRLRTLEQAPLWLYPLDGAAWAALDRLWDAL 233 Query: 247 TKGKKSLSLNISTE--GGYEIHVPFFCSRVSRFSFFDLCDRPLSANDFVEIANRFDVVII 304 T G+ +ST + FSF DLC P +D++ +A RF V + Sbjct: 234 TLGEPQ---PLSTLEVAARLARARAAGGDLVWFSFADLCLAPRHPSDYLALAERFSTVFL 290 Query: 305 NDIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDLFPYKLRKGAFEIQRTVSR 364 D+P + +D +RFI L+D Y+ + L+ S+E ++DL+ AFE QRT+SR Sbjct: 291 TDVPPMTRCSQDEARRFIALVDELYDRHVKLVASAEAALDDLYRGGR--LAFEFQRTLSR 348 Query: 365 LYEMFSAQYIGK 376 L EM S Y+ + Sbjct: 349 LLEMQSEDYLAR 360 >gnl|CDD|37594 KOG2383, KOG2383, KOG2383, Predicted ATPase [General function prediction only]. Length = 467 Score = 273 bits (700), Expect = 5e-74 Identities = 141/419 (33%), Positives = 215/419 (51%), Gaps = 56/419 (13%) Query: 12 SLIQDKKLKYNPAQESVVKSFDRL---LVDLY----KQQKQEQGIFSWLWNLR------- 57 L+ LK +P Q V +F+RL L++ Y KQ ++ W++ L+ Sbjct: 42 KLVNTGTLKSDPYQRKTVSAFERLYHELIEYYDPRLKQWSAKREEGRWIFELKKSFDDGK 101 Query: 58 ----GIKRKYCSMQGIYLHGDVGQGKSMLMNLFF-ALVPIEKKCRLHFYEFMKDVHSRII 112 + +G+YL+G VG GK+MLM+LF+ AL PI +K R+HF+ FM VH R+ Sbjct: 102 LDTPNASGQPGPPKGLYLYGSVGCGKTMLMDLFYDALPPIWRKQRVHFHGFMLSVHKRMH 161 Query: 113 MYRK-----KIEFGEILESDPIPLVASSIALESRVLCFDEFMITNIADAIILSRLFAALF 167 ++ K + + E DP+P+VA IA E+ +LCFDEF +T++ADA+IL RLF LF Sbjct: 162 ELKQEQGAEKPGYAKSWEIDPLPVVADEIAEEAILLCFDEFQVTDVADAMILKRLFEHLF 221 Query: 168 SHGCIIVMTSNFIPENLYKDEINRNVLVSFIELLEKKLEIISLDSGQDYRRKEQSILPIY 227 +G ++V TSN PE+LYK+ + R + FI LLE++ ++I LDSG DYRRK +S Y Sbjct: 222 KNGVVLVATSNRAPEDLYKNGLQRENFIPFIALLEERCKVIQLDSGVDYRRKAKSAGENY 281 Query: 228 MTPLNSYNRVLMDKLW-AHITKGKKSLSLNISTEGGYEIHVPFFCSRVSRFSFFDLCDRP 286 + ++ + + G ++ VP C V+ F+F +LC RP Sbjct: 282 YFISETDVETVLKEWFKLLAADQNDGTRQRTLVVFGRKLIVPKACGGVADFTFEELCGRP 341 Query: 287 LSANDFVEIANRFDVVIINDIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDL 346 L A D++ +A F +I+ DIP L + +D +RFI LID Y++ + L+ S+ +E+L Sbjct: 342 LGAADYLGLAKNFHTIIVRDIPQLSLENRDQARRFITLIDALYDNHVRLVCSAATPLEEL 401 Query: 347 FPYK------------LRKG-------------------AFEIQRTVSRLYEMFSAQYI 374 F + L F RT+SRLYEM + Y Sbjct: 402 FQFTGHSEALSDSPRTLMDDLGIKSDSAGGSPMFSGEEEGFAFDRTLSRLYEMQTELYW 460 >gnl|CDD|37256 KOG2045, KOG2045, KOG2045, 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning]. Length = 1493 Score = 29.3 bits (65), Expect = 1.7 Identities = 14/83 (16%), Positives = 25/83 (30%), Gaps = 5/83 (6%) Query: 269 FFCSRVSRFSFFDLCDRPLSANDFVEIANRFDVVIINDIPLLKEDRKDWIK-----RFIM 323 S D D ++F + +ND ++ W K F Sbjct: 424 LEPGSGSDELLLDNLDADELEDEFAVELATLALSGMNDADFANDEEACWEKTILNKEFQR 483 Query: 324 LIDVFYEHKIGLIISSEENIEDL 346 +Y K+ + EE + +L Sbjct: 484 WKRNYYRDKLKFDPNDEELLREL 506 >gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.. Length = 157 Score = 29.1 bits (65), Expect = 2.4 Identities = 23/115 (20%), Positives = 41/115 (35%), Gaps = 9/115 (7%) Query: 73 GDVGQGKSMLMNLFFALV-PIEKKCRLHFYEFMKDVHS---RIIMYRKKIEFGEILESDP 128 G G GKS L+ L+ P + + + K R I Y ++ G+ Sbjct: 32 GPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRV-- 89 Query: 129 IPLVASSIALESRVLCFDEFMI-TNIADAIILSRLFAALFSHGCIIVMTSNFIPE 182 +A ++ L +L DE + A L L L G +++ ++ Sbjct: 90 --ALARALLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPEL 142 >gnl|CDD|30938 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]. Length = 408 Score = 28.7 bits (64), Expect = 3.1 Identities = 27/122 (22%), Positives = 45/122 (36%), Gaps = 21/122 (17%) Query: 69 IYLHGDVGQGKSMLM----NLFFALVPIEKKCRLHFYEFMKDVHSRIIMYRKKIEFGEIL 124 ++++G VG GK+ L+ N A P + L +F D + + +F E Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVK-ALRDNEMEKFKEKY 174 Query: 125 ESDPIPLVASSIALESRVLCFDEFMITNIADAI--ILSRLFAALFSHGCIIVMTSNFIPE 182 D +L D+ + F AL +G IV+TS+ P+ Sbjct: 175 SLD--------------LLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPK 220 Query: 183 NL 184 L Sbjct: 221 EL 222 >gnl|CDD|144489 pfam00910, RNA_helicase, RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses. Length = 105 Score = 28.0 bits (63), Expect = 4.5 Identities = 8/18 (44%), Positives = 10/18 (55%) Query: 69 IYLHGDVGQGKSMLMNLF 86 I+L+G G GKS L Sbjct: 1 IWLYGPPGCGKSTLAKYL 18 >gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. Length = 212 Score = 27.9 bits (62), Expect = 4.8 Identities = 14/54 (25%), Positives = 25/54 (46%) Query: 294 EIANRFDVVIINDIPLLKEDRKDWIKRFIMLIDVFYEHKIGLIISSEENIEDLF 347 +AN V+I ++P + D + +L D H++GLI +I L+ Sbjct: 23 AMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLY 76 >gnl|CDD|144176 pfam00483, NTP_transferase, Nucleotidyl transferase. This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars. Length = 247 Score = 27.6 bits (62), Expect = 7.5 Identities = 8/53 (15%), Positives = 19/53 (35%), Gaps = 6/53 (11%) Query: 152 NIADAIILSRLFAALFSHGCIIVMTSNFIPENLYKD------EINRNVLVSFI 198 A A+ L+ F ++V+ + I +++ + V+F Sbjct: 85 GTAPAVALAADFLGDDDPELVLVLGGDHIYRMDFEEAVQKARAKAADGTVTFG 137 >gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and metabolism]. Length = 191 Score = 27.4 bits (61), Expect = 7.8 Identities = 9/25 (36%), Positives = 14/25 (56%) Query: 282 LCDRPLSANDFVEIANRFDVVIIND 306 + R +A + A+ FD VI+ND Sbjct: 143 IARRLENAKKEISHADEFDYVIVND 167 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 0.326 0.142 0.414 Gapped Lambda K H 0.267 0.0579 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,999,221 Number of extensions: 279595 Number of successful extensions: 978 Number of sequences better than 10.0: 1 Number of HSP's gapped: 968 Number of HSP's successfully gapped: 20 Length of query: 404 Length of database: 6,263,737 Length adjustment: 96 Effective length of query: 308 Effective length of database: 4,189,273 Effective search space: 1290296084 Effective search space used: 1290296084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 58 (26.5 bits)