RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780630|ref|YP_003065043.1| ribonuclease PH [Candidatus Liberibacter asiaticus str. psy62] (242 letters) >gnl|CDD|31033 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis]. Length = 230 Score = 247 bits (632), Expect = 2e-66 Identities = 114/240 (47%), Positives = 156/240 (65%), Gaps = 18/240 (7%) Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTAT-LEEKVPMWIRNTKHGWI 59 MR GR+ +++R I +TR V K+AEGS L++FG+T ++ T + E VP ++R T GW+ Sbjct: 8 MRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWL 67 Query: 60 TAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVI 119 TAEYGMLPRST R KREA GR ++EI R+IGRALR+V+DL L I IDCDV+ Sbjct: 68 TAEYGMLPRSTDERKKREADRGR----TKEISRLIGRALRAVIDLELLPESTIDIDCDVL 123 Query: 120 QADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDY 179 QADGGTRTA+ITGA +AL D + D VAAIS G++ G ++DLDY Sbjct: 124 QADGGTRTASITGASLALADAGIPLRDL-------------VAAISVGIVDGVIVLDLDY 170 Query: 180 GEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDVIS 239 EDS + D N VMT +G +VE+QG AE F++D +L+LA +L +LQ++ ++ Sbjct: 171 EEDSAAEADMNVVMTGNGGLVEIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREALA 230 >gnl|CDD|144653 pfam01138, RNase_PH, 3' exoribonuclease family, domain 1. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 128 Score = 120 bits (304), Expect = 3e-28 Identities = 47/130 (36%), Positives = 63/130 (48%), Gaps = 6/130 (4%) Query: 10 QMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWITAEYGMLPRS 69 ++R I + V A+GS LV+ GDT +L T T + P R+ G +T EY P + Sbjct: 1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPPNE-RDFFPGELTVEYEEKPFA 59 Query: 70 TGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQADGGTRTAA 129 +G R GR R E+ R+I RALR L +I ID V+ DG AA Sbjct: 60 SGERP-----EGRPSEREIELSRLIDRALRPSFPLEGYPRWEIRIDITVLSDDGSLLDAA 114 Query: 130 ITGAWVALHD 139 I A +AL D Sbjct: 115 INAASLALAD 124 >gnl|CDD|36286 KOG1068, KOG1068, KOG1068, Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]. Length = 245 Score = 84.6 bits (209), Expect = 2e-17 Identities = 58/242 (23%), Positives = 93/242 (38%), Gaps = 26/242 (10%) Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTT-ATLEEKVPMWIRNTKHGWIT 60 R GR+ N++R I V A+GS ++ G+T +L E R + Sbjct: 14 RTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLN 73 Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQ 120 E STG+R KR + R +E+ M+ +A V+ L QI I V++ Sbjct: 74 CEVSSAQFSTGDRKKRP----KGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLE 129 Query: 121 ADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVDLDYG 180 DG AAI A +AL D M D + A + G+ G P++DL Sbjct: 130 DDGSNLAAAINAATLALADAGIPMYDL-------------ITACTAGLADGTPLLDLTSL 176 Query: 181 EDSTIDVD---ANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKLQKDV 237 E+S A + ++++ DH +L LA + + + V Sbjct: 177 EESARAPGLTVAALPNREEIALLQLDER-----LHCDHLETVLELAIAGCKRVYERLRLV 231 Query: 238 IS 239 + Sbjct: 232 LR 233 >gnl|CDD|32306 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]. Length = 272 Score = 69.2 bits (169), Expect = 1e-12 Identities = 49/257 (19%), Positives = 93/257 (36%), Gaps = 26/257 (10%) Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKH-GWIT 60 R+ GR ++ R + + V A GS LVK G+T ++ E P +T + G + Sbjct: 24 RIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEIGEPF--PDTPNEGVLV 81 Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSV--VDLSALGSRQ------I 112 + P ++ + E G + E+ R++ R LR +DL L + + Sbjct: 82 VNVELSPLASPS---FEP--GPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWVV 136 Query: 113 IIDCDVIQADGGTRTAAITGAWVAL---------HDCLQHMEDCSNKFQLSQVLKGHVAA 163 +D V+ DG AA A AL + + + + + Sbjct: 137 FVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPIS 196 Query: 164 ISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLA 223 ++ + +VD E+ D + + G IV +Q + ++ L A Sbjct: 197 VTFAKIGNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQ-KVGGGSITESDLEKALKTA 255 Query: 224 KDRIADLIKLQKDVISN 240 + L + K+ + Sbjct: 256 LSKAEKLREALKEALKE 272 >gnl|CDD|146389 pfam03725, RNase_PH_C, 3' exoribonuclease family, domain 2. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. Length = 67 Score = 54.5 bits (132), Expect = 2e-08 Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 1/68 (1%) Query: 159 GHVAAISCGMLCGYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFA 218 G VAA++ G + G ++D E+S D D V+ +G IV + +++ Sbjct: 1 GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGDIVALM-KEGGGGLTEEELLE 59 Query: 219 MLNLAKDR 226 L LA Sbjct: 60 ALELAHKG 67 >gnl|CDD|36285 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]. Length = 760 Score = 44.2 bits (104), Expect = 3e-05 Identities = 58/238 (24%), Positives = 100/238 (42%), Gaps = 42/238 (17%) Query: 12 REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEK------VPMWIRNTKHGWITAEYG 64 REI T +++++A GS +V+ G+T ++TT L +K +P+ + + A G Sbjct: 56 REILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPPQFLPLVV---DYQEKFAAVG 112 Query: 65 MLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDCDVIQADG- 123 +P GN ++RE GR + R+I R +R + QI+ C+V+ +DG Sbjct: 113 RIP---GNFMRRE---GRTKDKEILTGRLIDRPIRPLFPKGFYHETQIL--CNVLSSDGV 164 Query: 124 -GTRTAAITGAWVALHDCLQHMEDCSNKFQLSQV-LKGHVAAISCGMLCGYPIVDLDYGE 181 AI A AL LS V G + A+ G++ G +V+ E Sbjct: 165 HDPDVLAINAASAAL--------------SLSDVPWNGPIGAVRIGLIDGEFVVNPTRKE 210 Query: 182 DSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDR----IADLIKLQK 235 S+ ++ T S V ++GS+ Q + + I + +L K Sbjct: 211 MSSSQLNLVVAGTKS-QTVMLEGSSN--NILQQDLLHAIKVGVKEAQQIIQGIERLAK 265 Score = 43.1 bits (101), Expect = 7e-05 Identities = 43/186 (23%), Positives = 74/186 (39%), Gaps = 27/186 (14%) Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLE-----EKVPMWIRNTKH 56 R GR +++R IS + K GS L + G T +L T TL+ +K+ I Sbjct: 359 RCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLESAQKLDSLIGPDNG 418 Query: 57 GWITAEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQIIIDC 116 Y P +T K ++ R+ G + +AL V L I + Sbjct: 419 INFMLHYEFPPYATNEVGKIGGLNRRELGHGA----LAEKALLPV--LPEDFPFTIRVTS 472 Query: 117 DVIQADGGTRTAAITGAWVALHDCLQHMEDCSNKFQLSQVLKGHVAAISCGMLCGYPIVD 176 +V++++G + A++ G +AL D + HVA ++ G++ D Sbjct: 473 EVLESNGSSSMASVCGGSLALMDA-------------GVPVSAHVAGVAIGLVTK---TD 516 Query: 177 LDYGED 182 + GE Sbjct: 517 PEKGEI 522 >gnl|CDD|36827 KOG1614, KOG1614, KOG1614, Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis]. Length = 291 Score = 43.4 bits (102), Expect = 5e-05 Identities = 52/262 (19%), Positives = 90/262 (34%), Gaps = 34/262 (12%) Query: 2 RLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGW-IT 60 R GR + R++ + GS LV G+T ++ T + P R + + I Sbjct: 23 RFDGRSLEEFRDLEIEFGKEY---GSVLVTMGNTKVMARVTAQIAQPYIDRPHEGSFSIF 79 Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSALGSR------QI 112 E + + GR+G E+ R+I +ALR +D +L R I Sbjct: 80 TELSPMASPSFE-------PGRKGESEVELSRLIEKALRRSKAIDTESLCIRAGEKVWLI 132 Query: 113 IIDCDVIQADGGTRTAAITGAWVALH-----DCLQHMEDCSNKFQLSQV---LKGHVAAI 164 ID ++ DG AA AL D E+ + L H I Sbjct: 133 RIDLHILDHDGNLVDAACIAVIAALMHFRRPDVTVGGEEVIIHPVEEREPVPLSIHHMPI 192 Query: 165 SCGMLC-----GYPIVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAM 219 C ++D E++ +D M + + +Q + + Sbjct: 193 -CFTFGFFNKGEIVVIDPTEKEEAVMDGSMVVTMNKNREVCAIQ-KSGGEILDESVIERC 250 Query: 220 LNLAKDRIADLIKLQKDVISNE 241 LAKDR ++ + + + + Sbjct: 251 YKLAKDRAVEVTGIILEALEED 272 >gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]. Length = 692 Score = 38.2 bits (89), Expect = 0.002 Identities = 52/243 (21%), Positives = 89/243 (36%), Gaps = 54/243 (22%) Query: 12 REISL-TRRVSKYAEGSCLVKFGDTHLLTTATLEEK------VPMWIRNTKHGWITAEY- 63 R ++L T ++++ A G+ LV++GDT +L T + P+ T Y Sbjct: 14 RTLTLETGKIARQANGAVLVRYGDTVVLATVVASKPKEGQDFFPL----------TVNYE 63 Query: 64 ------GMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRSVVDLSALGSRQ-IIIDC 116 G +P G KRE GR + R+I R +R L G R + I Sbjct: 64 EKTYAAGKIP---GGFFKRE---GRPSEKEILTSRLIDRPIRP---LFPKGFRNEVQIVN 114 Query: 117 DVIQADGGT--RTAAITGAWVALHDCLQHMEDCSNKFQLSQV-LKGHVAAISCGMLCGYP 173 V+ D A+ GA AL LS + G + A+ G + G Sbjct: 115 TVLSVDPENDPDILAMVGASAALS--------------LSGIPFLGPIGAVRVGYIDGIF 160 Query: 174 IVDLDYGEDSTIDVDANFVMTDSGHIVEVQGSAERATFSQDHFFAMLNLAKDRIADLIKL 233 +++ E +D V + V+ A+ ++ + + I +I Sbjct: 161 VLNPTLEELEESKLD-LVVAGTKDAVNMVESEAD--ELDEEVMLEAVEFGHEAIQSVINA 217 Query: 234 QKD 236 Q++ Sbjct: 218 QEE 220 >gnl|CDD|36826 KOG1613, KOG1613, KOG1613, Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]. Length = 298 Score = 33.8 bits (77), Expect = 0.042 Identities = 32/153 (20%), Positives = 58/153 (37%), Gaps = 18/153 (11%) Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDTHLLTTATLEEKVPMWIRNTKHGWIT 60 +R GR+ + R+ ++ A GS L+K G T ++ E P G I Sbjct: 36 IRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICGIKAEIAEPS-TDAPDEGDIV 94 Query: 61 AEYGMLPRSTGNRVKREAVSGRQGGRSQEIQRMIGRALRS--VVDLSAL----GSRQIII 114 Y + P + +R + G +Q I + + + ++ AL G ++ Sbjct: 95 PNYALPPLCS-SRFR----PGPPTDEAQVISQKLHDTILHSRIIPKKALCIKAGKAAWVL 149 Query: 115 DCDVI--QADGGTRTAAITGAWVALHDCLQHME 145 D+I DG W AL L++++ Sbjct: 150 YADIICLDYDG----PVFDACWNALMAALKNVK 178 >gnl|CDD|58274 cd01434, EFG_mtEFG1_IV, EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG2s are not present in this group.. Length = 116 Score = 29.2 bits (66), Expect = 1.00 Identities = 11/22 (50%), Positives = 14/22 (63%) Query: 156 VLKGHVAAISCGMLCGYPIVDL 177 V KG A+ G L GYP+VD+ Sbjct: 60 VEKGFREALEKGPLAGYPVVDV 81 >gnl|CDD|36825 KOG1612, KOG1612, KOG1612, Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]. Length = 288 Score = 27.3 bits (60), Expect = 3.6 Identities = 13/35 (37%), Positives = 16/35 (45%) Query: 1 MRLSGRQENQMREISLTRRVSKYAEGSCLVKFGDT 35 +R GR +Q R I + V GS VK GD Sbjct: 21 IRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDG 55 >gnl|CDD|30828 COG0480, FusA, Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]. Length = 697 Score = 26.0 bits (57), Expect = 8.8 Identities = 11/25 (44%), Positives = 15/25 (60%) Query: 153 LSQVLKGHVAAISCGMLCGYPIVDL 177 + V KG A+ G L GYP+VD+ Sbjct: 537 IPAVEKGFREALKSGPLAGYPVVDV 561 >gnl|CDD|146417 pfam03764, EFG_IV, Elongation factor G, domain IV. This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. Length = 120 Score = 26.0 bits (58), Expect = 9.1 Identities = 9/22 (40%), Positives = 12/22 (54%) Query: 156 VLKGHVAAISCGMLCGYPIVDL 177 V KG A+ G L G P+ D+ Sbjct: 64 VEKGFQEAMKEGPLAGEPVRDV 85 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 0.321 0.134 0.393 Gapped Lambda K H 0.267 0.0789 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,722,257 Number of extensions: 134015 Number of successful extensions: 298 Number of sequences better than 10.0: 1 Number of HSP's gapped: 289 Number of HSP's successfully gapped: 18 Length of query: 242 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 151 Effective length of database: 4,297,318 Effective search space: 648895018 Effective search space used: 648895018 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: 56 (25.2 bits)