RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780751|ref|YP_003065164.1| ribonuclease E [Candidatus Liberibacter asiaticus str. psy62] (723 letters) >gnl|CDD|31719 COG1530, CafA, Ribonucleases G and E [Translation, ribosomal structure and biogenesis]. Length = 487 Score = 397 bits (1022), Expect = e-111 Identities = 184/385 (47%), Positives = 250/385 (64%) Query: 170 IQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDR 229 I+ ++ Q LVQ+VKE RG KGA +TT +SLAGRY VLMPN ISR+I ++R Sbjct: 84 IKVRLRGGQATLVQVVKEPRGTKGARLTTDISLAGRYLVLMPNAPDVGGISRRIEGEIER 143 Query: 230 KNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHLVY 289 + LKEI R L P GMG+I+RTAG ++ E++RD +YL RLW+ + E A AP L+Y Sbjct: 144 ERLKEIVRELVDPGGMGLIIRTAGEGASEEELRRDLDYLRRLWEAILERAKKRPAPGLLY 203 Query: 290 EEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRS 349 EE +L+ R IRD KDI+EI+V G++ Y EAK+F+ +MP ++ Y P+F Sbjct: 204 EETSLVVRVIRDYVGKDITEIVVDGKEAYLEAKEFILEIMPELRSKLKLYRGTTPLFALF 263 Query: 350 GIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIEDTALQTNLEAAEE 409 GIE Q+ + +V LPS GY++I+ TEAL IDVNSGR T +E+TA+ TNLEAAEE Sbjct: 264 GIEEQIARALERKVQLPSGGYLVIDPTEALTVIDVNSGRFTGAGDLEETAVNTNLEAAEE 323 Query: 410 IARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSR 469 IARQLRLR+L G+I++DFIDM E+ + R V ++L+ +LK+DRAR+Q+G IS GLLEM+R Sbjct: 324 IARQLRLRNLGGIIIIDFIDMTEESHQRLVLERLRRALKRDRARIQIGRISELGLLEMTR 383 Query: 470 QRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAHNIIVHTHSDVVL 529 +R R S+LE ++ C CKG G++RS S L ILR +EE + V V Sbjct: 384 KRTRESLLEVLSERCPGCKGTGHVRSTESELLHILRYIEEEADINKTPEVGVEVPPAVAK 443 Query: 530 YLLNQKRATIVEYEARFGVSINVVI 554 YLLN++R I E E G + Sbjct: 444 YLLNEERGAIAELELFKGYLRVRLR 468 Score = 102 bits (256), Expect = 3e-22 Identities = 43/90 (47%), Positives = 56/90 (62%), Gaps = 1/90 (1%) Query: 3 NKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYG 62 KMLI+A+ EETRV V+ ++ELD E K+QI GNIY +VTRV PSL+AAFVD G Sbjct: 2 KKMLINATQ-EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIG 60 Query: 63 GNRHGFLPFLEIHPDYYQIPFSDRQALLKE 92 R+GFL EI P + + + L+ Sbjct: 61 LERNGFLHLSEIVPYFRAVLEEKIKVRLRG 90 >gnl|CDD|88419 cd04453, S1_RNase_E, S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.. Length = 88 Score = 67.2 bits (164), Expect = 2e-11 Identities = 22/47 (46%), Positives = 32/47 (68%) Query: 33 EHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYY 79 +++ I GNIYL +V ++ P LQAAFVD G ++GFL +I P Y+ Sbjct: 1 PNREPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYF 47 Score = 54.1 bits (130), Expect = 1e-07 Identities = 21/46 (45%), Positives = 30/46 (65%) Query: 160 VPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGR 205 +P FK+ I +++K Q +LVQ+VKE G KG +TT +SL GR Sbjct: 43 LPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLTTNISLPGR 88 >gnl|CDD|144242 pfam00575, S1, S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Length = 74 Score = 38.4 bits (90), Expect = 0.007 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 2/47 (4%) Query: 36 KQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIP 82 K +G++ VTRV AFVD G GF+P EI D + P Sbjct: 1 KPEEGDVVKGTVTRVTK--GGAFVDLGNGVEGFIPISEISDDRVEDP 45 >gnl|CDD|33156 COG3347, COG3347, Uncharacterized conserved protein [Function unknown]. Length = 404 Score = 32.6 bits (74), Expect = 0.38 Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 6/105 (5%) Query: 506 SVEEYLLQYTAHNIIVHTHSDVVLYLLNQK--RATIVE-YEARFGVSINVVIGIELA--- 559 S+E L + ++ HTH+D ++ + Q +A I E + R V G LA Sbjct: 114 SIETLLHAFLPFKVVDHTHADAIIAIAVQANGKALIREIFGDRVVWVPYVRPGFPLAKAI 173 Query: 560 DKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALL 604 + F + L N G D+ +Y++ I V + E L Sbjct: 174 AERFKANPDAEGLVLENHGLFTFGDTAKEAYERMISIVNEAEEYL 218 >gnl|CDD|145880 pfam02956, TT_ORF1, TT viral orf 1. TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. Length = 525 Score = 31.5 bits (72), Expect = 0.95 Identities = 9/12 (75%), Positives = 10/12 (83%) Query: 629 RKRRRRRRRRRP 640 R+RRR RRRRR Sbjct: 29 RRRRRVRRRRRG 40 Score = 30.3 bits (69), Expect = 2.0 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 627 VIRKRRRRRRRRRP 640 V R+RR RRRRRR Sbjct: 34 VRRRRRGRRRRRRR 47 Score = 29.9 bits (68), Expect = 2.5 Identities = 10/11 (90%), Positives = 11/11 (100%) Query: 629 RKRRRRRRRRR 639 R+RRRRRRRRR Sbjct: 46 RRRRRRRRRRR 56 Score = 29.9 bits (68), Expect = 2.8 Identities = 9/12 (75%), Positives = 10/12 (83%) Query: 629 RKRRRRRRRRRP 640 R+RR RRRRRR Sbjct: 21 RRRRARRRRRRR 32 Score = 29.5 bits (67), Expect = 3.3 Identities = 10/11 (90%), Positives = 11/11 (100%) Query: 629 RKRRRRRRRRR 639 R+RRRRRRRRR Sbjct: 44 RRRRRRRRRRR 54 Score = 29.5 bits (67), Expect = 3.5 Identities = 9/11 (81%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R+RRRRR RRR Sbjct: 27 RRRRRRRVRRR 37 Score = 29.2 bits (66), Expect = 3.9 Identities = 10/12 (83%), Positives = 11/12 (91%) Query: 629 RKRRRRRRRRRP 640 R+RRRRRRRRR Sbjct: 42 RRRRRRRRRRRR 53 Score = 29.2 bits (66), Expect = 4.1 Identities = 9/11 (81%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R+RRRR RRRR Sbjct: 28 RRRRRRVRRRR 38 Score = 29.2 bits (66), Expect = 4.2 Identities = 9/11 (81%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R+ RRRRRRRR Sbjct: 23 RRARRRRRRRR 33 Score = 29.2 bits (66), Expect = 4.2 Identities = 11/14 (78%), Positives = 12/14 (85%) Query: 626 GVIRKRRRRRRRRR 639 G R+RRRRRRRRR Sbjct: 40 GRRRRRRRRRRRRR 53 Score = 29.2 bits (66), Expect = 4.2 Identities = 10/11 (90%), Positives = 11/11 (100%) Query: 629 RKRRRRRRRRR 639 R+RRRRRRRRR Sbjct: 45 RRRRRRRRRRR 55 Score = 29.2 bits (66), Expect = 4.3 Identities = 9/11 (81%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R+RRR RRRRR Sbjct: 20 RRRRRARRRRR 30 Score = 29.2 bits (66), Expect = 4.3 Identities = 9/11 (81%), Positives = 11/11 (100%) Query: 629 RKRRRRRRRRR 639 R+RRRRRRR+R Sbjct: 48 RRRRRRRRRKR 58 Score = 28.8 bits (65), Expect = 5.1 Identities = 9/11 (81%), Positives = 9/11 (81%) Query: 631 RRRRRRRRRPA 641 RRRRRRRR A Sbjct: 15 GRRRRRRRRRA 25 Score = 28.8 bits (65), Expect = 5.9 Identities = 10/11 (90%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R RRRRRRRRR Sbjct: 14 RGRRRRRRRRR 24 Score = 28.8 bits (65), Expect = 6.2 Identities = 9/12 (75%), Positives = 10/12 (83%) Query: 629 RKRRRRRRRRRP 640 R+R RRRRRRR Sbjct: 22 RRRARRRRRRRR 33 Score = 28.4 bits (64), Expect = 6.6 Identities = 9/11 (81%), Positives = 11/11 (100%) Query: 629 RKRRRRRRRRR 639 R+RRRRRRRR+ Sbjct: 47 RRRRRRRRRRK 57 Score = 28.4 bits (64), Expect = 6.6 Identities = 9/11 (81%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R+RRRRRR RR Sbjct: 26 RRRRRRRRVRR 36 Score = 28.0 bits (63), Expect = 9.2 Identities = 8/11 (72%), Positives = 9/11 (81%) Query: 629 RKRRRRRRRRR 639 R+R RRRRR R Sbjct: 31 RRRVRRRRRGR 41 Score = 28.0 bits (63), Expect = 9.7 Identities = 9/11 (81%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R+RRRRRRR R Sbjct: 16 RRRRRRRRRAR 26 Score = 28.0 bits (63), Expect = 9.7 Identities = 9/11 (81%), Positives = 10/11 (90%) Query: 629 RKRRRRRRRRR 639 R+RRRRRR RR Sbjct: 17 RRRRRRRRARR 27 >gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. Length = 363 Score = 30.7 bits (70), Expect = 1.5 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 15/67 (22%) Query: 401 QTNLEAAEEIARQL---RLRDLAGLIVVDFIDM-------EEKKNNR-----SVEKKLKE 445 + + E AEE+AR++ L +LA I +D +M EE +R V K +++ Sbjct: 104 KYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKAIEK 163 Query: 446 SLKKDRA 452 K Sbjct: 164 LKKGKVG 170 >gnl|CDD|119350 cd02871, GH18_chitinase_D-like, GH18 domain of Chitinase D (ChiD). ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins. The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18 (GH18) domain, a chitin-binding domain, and a fibronectin type III domain. The chitin-binding and fibronectin type III domains are located either N-terminal or C-terminal to the catalytic domain. This family includes exochitinase Chi36 from Bacillus cereus.. Length = 312 Score = 29.6 bits (67), Expect = 2.8 Identities = 9/36 (25%), Positives = 16/36 (44%), Gaps = 8/36 (22%) Query: 52 PSLQAAFVDYGGNRHGFLPFLE--------IHPDYY 79 P +Q + YGG +LP ++ ++ YY Sbjct: 158 PYVQGGYAAYGGIWGAYLPLIDNLRDDLTWLNVQYY 193 >gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions. Length = 158 Score = 29.5 bits (67), Expect = 3.5 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 5/67 (7%) Query: 405 EAAEEIARQL---RLRDLAGLIVVDFIDMEEKKNNRSVEKKLK-ESLKKDRARVQVG-AI 459 EA EE+ + L L+ + LI + D+ + + +KL E + R +Q A+ Sbjct: 84 EAKEELHKLLNEEELKGVPLLIFANKQDLPGALSVSELIEKLGLEKILGRRWHIQPCSAV 143 Query: 460 SNFGLLE 466 + GL E Sbjct: 144 TGDGLDE 150 >gnl|CDD|39760 KOG4560, KOG4560, KOG4560, Transcription factor IIIC box B binding (alpha) subunit [Transcription]. Length = 1897 Score = 28.9 bits (64), Expect = 4.6 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 1/66 (1%) Query: 575 VNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLEDIQDNIVSEES-TGVIRKRRR 633 V GH + K +E +DE + L+D+ + + + I+K R Sbjct: 430 VAVGHLGDLSKEDEIKKKALEIRCKDEPNITESTDVLLKDLPEIVTNARPIAFKIKKTRA 489 Query: 634 RRRRRR 639 + +R Sbjct: 490 ANQTQR 495 >gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]. Length = 692 Score = 28.2 bits (63), Expect = 8.0 Identities = 8/30 (26%), Positives = 13/30 (43%), Gaps = 2/30 (6%) Query: 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFL 69 G +Y V R+ AFV+ + G + Sbjct: 620 GEVYEGTVVRIVDF--GAFVELLPGKDGLV 647 >gnl|CDD|176553 cd08612, GDPD_GDE4, Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function has not yet been elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests GDE4 may play some distinct role from other members of the GDE family. Length = 300 Score = 28.3 bits (64), Expect = 8.0 Identities = 7/18 (38%), Positives = 10/18 (55%) Query: 67 GFLPFLEIHPDYYQIPFS 84 G LPF+ I + +IP Sbjct: 204 GLLPFIPIKESFLEIPMP 221 >gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion transport and metabolism]. Length = 653 Score = 28.3 bits (63), Expect = 8.6 Identities = 25/112 (22%), Positives = 44/112 (39%), Gaps = 2/112 (1%) Query: 402 TNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISN 461 TNLE + QL + ++ ++ ID +K+ R +KL + L V A Sbjct: 92 TNLERNLYLTLQLLELGIPMILALNMIDEAKKRGIRIDIEKLSKLLGV--PVVPTVAKRG 149 Query: 462 FGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQ 513 GL E+ R I + ++T + Y + + R + LL+ Sbjct: 150 EGLEELKRAIIELAESKTTPREVDYGEEIEEEIKELEALSEDPRWLAIKLLE 201 >gnl|CDD|36426 KOG1212, KOG1212, KOG1212, Amidases [Translation, ribosomal structure and biogenesis, Lipid transport and metabolism, Signal transduction mechanisms]. Length = 560 Score = 28.0 bits (62), Expect = 9.3 Identities = 16/91 (17%), Positives = 26/91 (28%), Gaps = 17/91 (18%) Query: 400 LQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAI 459 A E A ++ + V+K + K D R + + Sbjct: 9 FLLRQLALIEDAENRLIK-------------FRLLLSLRVKKAKSTAPKLDTTRNAILKL 55 Query: 460 SNFGLLEMSRQRIRSSVLESTTKVCTYCKGA 490 Q ++S L S +C YC A Sbjct: 56 D----ATELAQALQSGELTSVEVLCAYCHRA 82 >gnl|CDD|34812 COG5215, KAP95, Karyopherin (importin) beta [Intracellular trafficking and secretion]. Length = 858 Score = 28.1 bits (62), Expect = 9.8 Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 18/94 (19%) Query: 591 DKNIECVWQDEALLPIPKSESLEDIQDNIVSEESTGVIRKRRRRRR-------------- 636 K EC+ +L +E++Q N + +IR RRR Sbjct: 548 KKLDECISVLGQILATEDQLLVEELQSNYIG-VLEAIIRTRRRDIEDVEDQLMELFIRIL 606 Query: 637 -RRRPATDHHDAGVVSDVSSIQNVIDDSFDMYME 669 +P T D V + +S++ +++ F+ Y Sbjct: 607 ESTKPTTAFGD--VYTAISALSTSLEERFEQYAS 638 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 0.369 Gapped Lambda K H 0.267 0.0752 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,431,440 Number of extensions: 453919 Number of successful extensions: 1502 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1492 Number of HSP's successfully gapped: 57 Length of query: 723 Length of database: 6,263,737 Length adjustment: 101 Effective length of query: 622 Effective length of database: 4,081,228 Effective search space: 2538523816 Effective search space used: 2538523816 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: 61 (27.2 bits)