RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780784|ref|YP_003065197.1| polynucleotide phosphorylase/polyadenylase [Candidatus Liberibacter asiaticus str. psy62] (699 letters) >gnl|CDD|31378 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]. Length = 692 Score = 886 bits (2292), Expect = 0.0 Identities = 380/694 (54%), Positives = 507/694 (73%), Gaps = 4/694 (0%) Query: 1 MFDVHTVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT 60 MF+ IEW GR L LETG+IARQ++GAVL YG+TVVLATVV + K+GQDFFPLT Sbjct: 1 MFNKIVKTIEWGGRTLTLETGKIARQANGAVLVRYGDTVVLATVVASK-PKEGQDFFPLT 59 Query: 61 VNYQERTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQH 120 VNY+E+TYA GKIPGG+ +RE RP+E EIL SR+IDR IRPLF K ++NE Q++ V+ Sbjct: 60 VNYEEKTYAAGKIPGGFFKREGRPSEKEILTSRLIDRPIRPLFPKGFRNEVQIVNTVLSV 119 Query: 121 DLESSPHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDE-DQGSLDLFVS 179 D E+ P +++MV ASAAL LSG+PF GP+ +V YI+G +VLNP L+E ++ LDL V+ Sbjct: 120 DPENDPDILAMVGASAALSLSGIPFLGPIGAVRVGYIDGIFVLNPTLEELEESKLDLVVA 179 Query: 180 GTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDF-S 238 GT+DAV MVE EA++L E+V+L+A+ FGH + VI A +LA K+ ++ Sbjct: 180 GTKDAVNMVESEADELDEEVMLEAVEFGHEAIQSVINAQEELALEVGKKKWELEPPSLDE 239 Query: 239 KLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDI 298 +LE ++ + +++L+ + I EK R +D +K+K+ S E S + EI ++ E + Sbjct: 240 ELEAKVRDLAEDELKEAVGIREKQERSAALDAIKEKIEEELSGEEES-SLKEIKAILEKL 298 Query: 299 QAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTRE 358 + K VR ++L+ KVR+DGR + VR I +VG+L RTHGS+LF RG+TQA+VVVTLGT Sbjct: 299 EKKPVRRLILEGKVRIDGRFGDEVRPIGIEVGVLPRTHGSALFTRGETQALVVVTLGTPR 358 Query: 359 DEQYVDSLSGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQ 418 D Q +D L G + F++HYNF P + GE RMG+P RREIGHG LA RA+ PVLP + Sbjct: 359 DAQVIDILEGEYKKRFLLHYNFPPFSVGETGRMGSPGRREIGHGALAERALAPVLPSEEE 418 Query: 419 FPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSD 478 FPYT+R+VSEI ES+GSSSMA+VCG SLALMDAGVPI PVAGIAMGL+K+GD + +LSD Sbjct: 419 FPYTIRVVSEILESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLIKEGDKYAVLSD 478 Query: 479 ISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKV 538 I GDEDHLG MDFKVAGTD GITA+QMD+KI GI++ IM AL+QAK RLHIL M++ Sbjct: 479 ILGDEDHLGDMDFKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEA 538 Query: 539 LSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASS 598 +SE R +L + PR+E + I PD+IR+VIG GGK I+ I E+TG K++I+DDGTVKIA+S Sbjct: 539 ISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAAS 598 Query: 599 SLAEIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA 658 + A+E I +IT EV ++Y+G VV+++DFGAFV +DGLVHISQL+ ERV Sbjct: 599 DGESAKKAKERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVE 658 Query: 659 KTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQ 692 K DV+KEGD V VK+++ D +G+I+LS+K V + Sbjct: 659 KVEDVLKEGDEVKVKVIEIDKQGRIRLSIKAVLE 692 >gnl|CDD|36285 KOG1067, KOG1067, KOG1067, Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]. Length = 760 Score = 575 bits (1483), Expect = e-164 Identities = 277/706 (39%), Positives = 417/706 (59%), Gaps = 31/706 (4%) Query: 6 TVEIEWAGRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQE 65 +VEI + R + ETG++AR ++G+V+ GET V+ TVV Q F PL V+YQE Sbjct: 48 SVEIPFGNREILFETGKLARFANGSVVVQMGETAVMTTVVLADKPSPPQ-FLPLVVDYQE 106 Query: 66 RTYAVGKIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESS 125 + AVG+IPG ++RRE R + EIL R+IDR IRPLF K + +ETQ++ NV+ D Sbjct: 107 KFAAVGRIPGNFMRREGRTKDKEILTGRLIDRPIRPLFPKGFYHETQILCNVLSSDGVHD 166 Query: 126 PHVVSMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGS-LDLFVSGTQDA 184 P V+++ AASAAL LS +P+ GP+ ++ I+G++V+NP E S L+L V+GT+ Sbjct: 167 PDVLAINAASAALSLSDVPWNGPIGAVRIGLIDGEFVVNPTRKEMSSSQLNLVVAGTKSQ 226 Query: 185 VLMVELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAK---EPIVIDSKDFSKLE 241 +M+E +N + + +L AI G E + +I+ I +LAK K EP + D +L Sbjct: 227 TVMLEGSSNNILQQDLLHAIKVGVKEAQQIIQGIERLAKKYGKQKREPQKLFLPD-PELV 285 Query: 242 EEMSQMIKEDLRVSCFIPE--KYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQ 299 + + ++ E L K R + ++ ++ E EI+ F + Sbjct: 286 KHVHKLAMERLYAVFTDYSHDKISRDEAVNKIRLDDEDKVKEEFPEQEPSEIIESFNTVS 345 Query: 300 AKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTRED 359 KV R+ +L++ R DGRD + +R+IS +V +L+ HGS+LF RG TQ + VTL + E Sbjct: 346 KKVFRSRILEEGKRCDGRDLDELRNISCEVDMLKTLHGSALFQRGQTQVLCTVTLDSLES 405 Query: 360 EQYVDSLSGT-QRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQ 418 Q +DSL G +FM+HY F P AT EV ++G +RRE+GHG LA +A+ PVLP+ Sbjct: 406 AQKLDSLIGPDNGINFMLHYEFPPYATNEVGKIGGLNRRELGHGALAEKALLPVLPE--D 463 Query: 419 FPYTLRIVSEITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGD------- 471 FP+T+R+ SE+ ES+GSSSMA+VCG SLALMDAGVP+S VAG+A+GLV D Sbjct: 464 FPFTIRVTSEVLESNGSSSMASVCGGSLALMDAGVPVSAHVAGVAIGLVTKTDPEKGEIE 523 Query: 472 DFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHI 531 D+ IL+DI G ED+ G MDFK+AGT+ G+TA+ + +K I++ ALQ+A+ RL I Sbjct: 524 DYRILTDILGIEDYNGDMDFKIAGTNDGVTALGIPLK-------IVMEALQKAREARLQI 576 Query: 532 LNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDG 591 L+ M K ++ R E++P +E + + P + +IG GG + + I +TGA + D+G Sbjct: 577 LDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-DEG 635 Query: 592 TVKIASSSLAEIEAAREMIRSITDVP-----EVNKIYKGQVVKVMDFGAFVHFCGARDGL 646 T I + + A +E A+E I I E +Y + ++ D G V + GL Sbjct: 636 TFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYTATITEIRDTGVMVELYPMQQGL 695 Query: 647 VHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRGKIKLSMKVVDQ 692 +H SQL E++AK SD+++ G + VK ++ D RG I LS + + Sbjct: 696 LHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLSSRALLP 741 >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 = 121 bits (307), Expect = 5e-28 Identities = 54/136 (39%), Positives = 80/136 (58%), Gaps = 13/136 (9%) Query: 13 GRPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFP--LTVNYQERTYAV 70 RP+++ETG + Q+DG+ L G+T VLATV + +DFFP LTV Y+E+ +A Sbjct: 2 LRPIEIETG-VLSQADGSALVELGDTKVLATVTGPIEPPNERDFFPGELTVEYEEKPFAS 60 Query: 71 GKIPGGYLRRESRPTENEILISRMIDRSIRPLF--SKCYKNETQVIINVMQHDLESSPHV 128 G+ P G RP+E EI +SR+IDR++RP F + E ++ I V+ D S Sbjct: 61 GERPEG------RPSEREIELSRLIDRALRPSFPLEGYPRWEIRIDITVLSDD--GSLLD 112 Query: 129 VSMVAASAALMLSGLP 144 ++ AAS AL +G+P Sbjct: 113 AAINAASLALADAGIP 128 Score = 115 bits (291), Expect = 3e-26 Identities = 47/132 (35%), Positives = 62/132 (46%), Gaps = 6/132 (4%) Query: 323 RDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHYNFLP 382 R I + G+L + GS+L GDT+ + VT G E D G + Y P Sbjct: 3 RPIEIETGVLSQADGSALVELGDTKVLATVT-GPIEPPNERDFFPGE----LTVEYEEKP 57 Query: 383 CATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIVSEITESDGSSSMATVC 442 A+GE G PS REI RL RA+ P P + +RI + DGS A + Sbjct: 58 FASGERPE-GRPSEREIELSRLIDRALRPSFPLEGYPRWEIRIDITVLSDDGSLLDAAIN 116 Query: 443 GSSLALMDAGVP 454 +SLAL DAG+P Sbjct: 117 AASLALADAGIP 128 >gnl|CDD|88437 cd04472, S1_PNPase, S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.. Length = 68 Score = 102 bits (257), Expect = 3e-22 Identities = 41/68 (60%), Positives = 51/68 (75%) Query: 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD 679 KIY+G+VVK+ DFGAFV +DGLVHIS+LS ERV K DV+K GD V VK+++ DD Sbjct: 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD 60 Query: 680 RGKIKLSM 687 RG+I LS Sbjct: 61 RGRISLSR 68 >gnl|CDD|31033 COG0689, Rph, RNase PH [Translation, ribosomal structure and biogenesis]. Length = 230 Score = 96.9 bits (241), Expect = 2e-20 Identities = 68/239 (28%), Positives = 110/239 (46%), Gaps = 16/239 (6%) Query: 307 MLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSL 366 + +R DGR + +R I G+L+ GSSL G+T+ I V+ G RE L Sbjct: 3 ESEDGMRPDGRKPDELRPIKITRGVLKHAEGSSLIEFGNTKVICTVS-GPREPVPR--FL 59 Query: 367 SGTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTLRIV 426 GT + Y LP +T E + A R RL RA+ V+ P + + Sbjct: 60 RGTGKGWLTAEYGMLPRSTDERKKREADRGRTKEISRLIGRALRAVI-DLELLPESTIDI 118 Query: 427 S-EITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDH 485 ++ ++DG + A++ G+SLAL DAG+P+ VA I++G+V I+ D+ +ED Sbjct: 119 DCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIVDGV----IVLDLDYEEDS 174 Query: 486 LGHMDFKVAGTDSG----ITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLS 540 D V T +G I + D G +E+ ++ L A +G + + L+ Sbjct: 175 AAEADMNVVMTGNGGLVEIQGLAED---GPFTEDELLELLDLAIKGCNELRELQREALA 230 Score = 56.8 bits (137), Expect = 2e-08 Identities = 49/217 (22%), Positives = 89/217 (41%), Gaps = 12/217 (5%) Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLTVNYQERTYAVGKI 73 RP+K+ G + ++G+ L +G T V+ TV ++ F T G + Sbjct: 19 RPIKITRGVLKH-AEGSSLIEFGNTKVICTVS---GPREPVPRFLRGTGKGWLTAEYGML 74 Query: 74 PGGYLRRESRPTEN--EILISRMIDRSIRPLFSKCYKNETQVII--NVMQHDLESSPHVV 129 P R+ R + ISR+I R++R + E+ + I +V+Q D Sbjct: 75 PRSTDERKKREADRGRTKEISRLIGRALRAVIDLELLPESTIDIDCDVLQADG--GTRTA 132 Query: 130 SMVAASAALMLSGLPFEGPVVGAQVDYINGQYVLNPRLDEDQGSL-DLFVSGTQDAVLMV 188 S+ AS AL +G+P V V ++G VL+ +ED + D+ V T + +V Sbjct: 133 SITGASLALADAGIPLRDLVAAISVGIVDGVIVLDLDYEEDSAAEADMNVVMTGNG-GLV 191 Query: 189 ELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMC 225 E++ D ++ + + +L + Sbjct: 192 EIQGLAEDGPFTEDELLELLDLAIKGCNELRELQREA 228 >gnl|CDD|29003 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.. Length = 61 Score = 86.7 bits (215), Expect = 2e-17 Identities = 35/60 (58%), Positives = 47/60 (78%) Query: 551 PRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMI 610 PR+E M IPPD+IR+VIG GGK I+ I+E+TG K++I+DDGTV IA+S E A++MI Sbjct: 1 PRIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60 >gnl|CDD|88439 cd05684, S1_DHX8_helicase, S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.. Length = 79 Score = 85.6 bits (212), Expect = 4e-17 Identities = 47/80 (58%), Positives = 54/80 (67%), Gaps = 5/80 (6%) Query: 620 NKIYKGQVVKVMDFGAFVHFCGAR---DGLVHISQLSTE-RVAKTSDVVKEGDTVWVKLL 675 KIYKG+V +MDFG FV G + +GLVHISQLS E RVA SDVVK G V VK++ Sbjct: 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVI 60 Query: 676 DFDDRGKIKLSMKVVDQNTG 695 GKI LSMK VDQ+TG Sbjct: 61 SI-QNGKISLSMKDVDQDTG 79 >gnl|CDD|88447 cd05692, S1_RPS1_repeat_hs4, S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 69 Score = 75.7 bits (186), Expect = 4e-14 Identities = 34/67 (50%), Positives = 45/67 (67%) Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRG 681 + +G V ++ FGAFV G GLVHISQ++ +RV DV+KEGD V VK+L D RG Sbjct: 3 VVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG 62 Query: 682 KIKLSMK 688 +I LS+K Sbjct: 63 RISLSIK 69 >gnl|CDD|31295 COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]. Length = 129 Score = 75.3 bits (185), Expect = 6e-14 Identities = 30/81 (37%), Positives = 47/81 (58%) Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLD 676 +V KG++ + +GAFV G + GLVHIS+++ V D +K G V VK+LD Sbjct: 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLD 62 Query: 677 FDDRGKIKLSMKVVDQNTGKP 697 D+ GKI LS++ +++ K Sbjct: 63 IDENGKISLSIRKLEEEPEKQ 83 >gnl|CDD|88441 cd05686, S1_pNO40, S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.. Length = 73 Score = 73.4 bits (180), Expect = 2e-13 Identities = 32/73 (43%), Positives = 48/73 (65%), Gaps = 1/73 (1%) Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTERVAKTSDVVKEGDTVWVKLL 675 P + +I+KG+V V ++GAFV G R GLVH S +S+ RV S+VV G+ VWVK++ Sbjct: 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVI 60 Query: 676 DFDDRGKIKLSMK 688 + + K+KLS+ Sbjct: 61 GREMKDKMKLSLS 73 >gnl|CDD|36286 KOG1068, KOG1068, KOG1068, Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis]. Length = 245 Score = 69.2 bits (169), Expect = 4e-12 Identities = 56/243 (23%), Positives = 101/243 (41%), Gaps = 14/243 (5%) Query: 309 DKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSG 368 ++ +R DGR +R I A++G+L + GS+ +G+T+ + V G RE S Sbjct: 10 EEGLRTDGRRPNELRRIYARIGVLTQADGSAYMEQGNTKVLCAVY-GPREIRGK--SARR 66 Query: 369 TQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVLPQTAQFPYT-LRIVS 427 + + +TG+ + RRE + ++A PV+ +P + + I Sbjct: 67 PDKAVLNCEVSSAQFSTGDRKKRPKGDRREKELSLMLQQAFEPVI-LLELYPRSQIDIYV 125 Query: 428 EITESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLG 487 ++ E DGS+ A + ++LAL DAG+P+ + GL L D++ E+ Sbjct: 126 QVLEDDGSNLAAAINAATLALADAGIPMYDLITACTAGLADG----TPLLDLTSLEESAR 181 Query: 488 HMDFKVA--GTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQ 545 VA I +Q+D + + + L+ A G + + VL E Sbjct: 182 APGLTVAALPNREEIALLQLD---ERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKN 238 Query: 546 LGE 548 Sbjct: 239 AES 241 Score = 36.8 bits (85), Expect = 0.022 Identities = 42/220 (19%), Positives = 89/220 (40%), Gaps = 10/220 (4%) Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVVYDRSLKDGQDFFPLT--VNYQERTYAVG 71 R + G + Q+DG+ G T VL V R ++ P +N + + Sbjct: 24 RRIYARIG-VLTQADGSAYMEQGNTKVLCAVYGPREIRGKSARRPDKAVLNCE---VSSA 79 Query: 72 KIPGGYLRRESRPTENEILISRMIDRSIRPLFSKCYKNETQVIINVMQHDLESSPHVVSM 131 + G ++ + E +S M+ ++ P+ +Q+ I V + + S ++ Sbjct: 80 QFSTGDRKKRPKGDRREKELSLMLQQAFEPVILLELYPRSQIDIYVQVLEDDGSNLAAAI 139 Query: 132 VAASAALMLSGLPFEGPVVGAQVDYINGQYVLNP-RLDEDQGSLDLFVS--GTQDAVLMV 188 AA+ AL +G+P + +G +L+ L+E + L V+ ++ + ++ Sbjct: 140 NAATLALADAGIPMYDLITACTAGLADGTPLLDLTSLEESARAPGLTVAALPNREEIALL 199 Query: 189 ELEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKE 228 +L+ +L D + + CK V E + + + K Sbjct: 200 QLD-ERLHCDHLETVLELAIAGCKRVYERLRLVLREHLKN 238 >gnl|CDD|30885 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]. Length = 541 Score = 68.8 bits (168), Expect = 5e-12 Identities = 44/148 (29%), Positives = 74/148 (50%), Gaps = 11/148 (7%) Query: 549 FTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAARE 608 F P + P + +IG K + + + +D + S E E Sbjct: 131 FLPGSLVDVRPVRDLDPLIG---KELEFKILE------LDKKRNNVVLSRRAVLEEERSE 181 Query: 609 MIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGD 668 + + EV ++ +G V + D+GAFV G DGL+HIS++S +RV S+VVK GD Sbjct: 182 QREELLNKLEVGEVVEGVVKNITDYGAFVD-IGGVDGLLHISEISWKRVDHPSEVVKVGD 240 Query: 669 TVWVKLLDFD-DRGKIKLSMKVVDQNTG 695 V VK++ D +RG++ LS+K ++++ Sbjct: 241 EVKVKVISLDEERGRVSLSLKQLEEDPW 268 Score = 67.6 bits (165), Expect = 1e-11 Identities = 30/77 (38%), Positives = 46/77 (59%), Gaps = 1/77 (1%) Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677 V +G+V + D+GAFV +GLVH+S++S + S+VVK G V VK+LD Sbjct: 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDI 335 Query: 678 D-DRGKIKLSMKVVDQN 693 D +R +I L +K + +N Sbjct: 336 DPERRRISLGLKQLKEN 352 Score = 48.3 bits (115), Expect = 7e-06 Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 1/72 (1%) Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677 V + +G+V + DFGAFV G DGLVH+S LS +R + ++ K+GD V K+L Sbjct: 362 PVGDVVEGKVKSITDFGAFVELEGGIDGLVHLSDLSWDRPGEEAEKYKKGDEVEAKVLAV 421 Query: 678 D-DRGKIKLSMK 688 D ++ +I L +K Sbjct: 422 DKEKERISLGIK 433 Score = 43.3 bits (102), Expect = 2e-04 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 8/79 (10%) Query: 615 DVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674 + + + KG+V V D GAFV G +GL+ +S+LS DV+K GD V + Sbjct: 445 EKYKKGSVVKGKVKSVKDKGAFVELGGGVEGLIRLSELS-------RDVLKVGDEVEAVV 497 Query: 675 LDFDDR-GKIKLSMKVVDQ 692 + D + KI LS+K +++ Sbjct: 498 VSIDKKNRKILLSIKALER 516 Score = 39.9 bits (93), Expect = 0.003 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 4/73 (5%) Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLL- 675 E + KG VV + G V G +G++ IS+ S E V DVV+ GD V V +L Sbjct: 19 FEPGDVVKGTVVSIEKDGVLVDIGGKSEGVIPISEFSNEPVE---DVVQVGDEVEVLVLR 75 Query: 676 DFDDRGKIKLSMK 688 D G++ LS + Sbjct: 76 VEDGEGELVLSRR 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 = 64.6 bits (158), Expect = 9e-11 Identities = 30/73 (41%), Positives = 44/73 (60%), Gaps = 1/73 (1%) Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLD 676 PE + KG V +V GAFV +G + IS++S +RV +V+K GD V VK+L Sbjct: 2 PEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLK 61 Query: 677 FD-DRGKIKLSMK 688 D +RG+I LS++ Sbjct: 62 VDKERGRIILSIR 74 >gnl|CDD|88443 cd05688, S1_RPS1_repeat_ec3, S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 68 Score = 64.0 bits (156), Expect = 1e-10 Identities = 31/67 (46%), Positives = 40/67 (59%), Gaps = 2/67 (2%) Query: 621 KIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-D 679 + +G V + DFGAFV G DGL+HIS +S RV S+VV GD V VK+L D + Sbjct: 3 DVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKE 61 Query: 680 RGKIKLS 686 R +I L Sbjct: 62 RKRISLG 68 >gnl|CDD|32366 COG2183, Tex, Transcriptional accessory protein [Transcription]. Length = 780 Score = 64.1 bits (156), Expect = 1e-10 Identities = 40/92 (43%), Positives = 57/92 (61%), Gaps = 2/92 (2%) Query: 607 REMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKE 666 E + SITD+ + I +G V V+DFGAFV +DGLVHISQLS + V ++VVK Sbjct: 647 DEGVESITDL-KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKV 705 Query: 667 GDTVWVKLLDFD-DRGKIKLSMKVVDQNTGKP 697 GD V VK+++ D R +I LSM++ ++ Sbjct: 706 GDIVKVKVIEVDTARKRIALSMRLDEEEGKLN 737 >gnl|CDD|31290 COG1093, SUI2, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]. Length = 269 Score = 62.2 bits (151), Expect = 4e-10 Identities = 32/88 (36%), Positives = 48/88 (54%), Gaps = 3/88 (3%) Query: 609 MIRSITDVPEVNKIYKGQVVKVMDFGAFVHF--CGARDGLVHISQLSTERVAKTSDVVKE 666 M + PE +I G V +V D+GA+V ++G +HIS++++ V D VKE Sbjct: 1 MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKE 60 Query: 667 GDTVWVKLLDFD-DRGKIKLSMKVVDQN 693 G V K+L D RG I LS+K V ++ Sbjct: 61 GQKVVAKVLRVDPKRGHIDLSLKRVTEH 88 >gnl|CDD|88440 cd05685, S1_Tex, S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.. Length = 68 Score = 58.3 bits (141), Expect = 7e-09 Identities = 31/66 (46%), Positives = 43/66 (65%), Gaps = 1/66 (1%) Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-DR 680 + +G V V DFGAFV +DGL+HIS+++ V+ SDVV GD V VK++ D +R Sbjct: 3 VLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEER 62 Query: 681 GKIKLS 686 G+I LS Sbjct: 63 GRISLS 68 >gnl|CDD|143804 pfam00013, KH_1, KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;. Length = 57 Score = 57.9 bits (141), Expect = 9e-09 Identities = 24/58 (41%), Positives = 34/58 (58%), Gaps = 1/58 (1%) Query: 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMI 610 E + IP + +IG GG I+ I E+TGAK+ I D TV I S + +E A+E+I Sbjct: 1 TEEILIPSSLVGRIIGKGGSNIKEIREETGAKIRIPDRDTVTI-SGTPEAVEKAKELI 57 >gnl|CDD|88416 cd00164, S1_like, S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.. Length = 65 Score = 57.7 bits (139), Expect = 1e-08 Identities = 30/65 (46%), Positives = 39/65 (60%), Gaps = 1/65 (1%) Query: 623 YKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDR-G 681 G+VV + FG FV +GLVHIS+LS + V S+V K GD V VK+L+ D G Sbjct: 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKG 60 Query: 682 KIKLS 686 +I LS Sbjct: 61 RISLS 65 >gnl|CDD|88418 cd04452, S1_IF2_alpha, S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.. Length = 76 Score = 55.1 bits (133), Expect = 7e-08 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 3/75 (4%) Query: 617 PEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674 PE ++ V + D GA+V G +G++ +S+LS R+ +VK G VK+ Sbjct: 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKV 60 Query: 675 LDFD-DRGKIKLSMK 688 + D ++G I LS K Sbjct: 61 IRVDKEKGYIDLSKK 75 >gnl|CDD|88427 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.. Length = 83 Score = 54.4 bits (131), Expect = 9e-08 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 2/83 (2%) Query: 606 AREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVK 665 + + +D+ + + G V + +G FV F G GL S +S E V S K Sbjct: 2 EGTLPTNFSDL-KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFK 60 Query: 666 EGDTVWVKLLDFD-DRGKIKLSM 687 +G +V K+ D ++ + LS+ Sbjct: 61 KGQSVTAKVTSVDEEKQRFLLSL 83 >gnl|CDD|146390 pfam03726, PNPase, Polyribonucleotide nucleotidyltransferase, RNA binding domain. This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction. Length = 80 Score = 51.9 bits (125), Expect = 6e-07 Identities = 28/80 (35%), Positives = 49/80 (61%) Query: 239 KLEEEMSQMIKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDI 298 +LEE+++ + +E L + I K R +D++K +V+ F+ E +E EI +F+ + Sbjct: 1 ELEEKVAALAEERLSEAYTITGKQERYAALDEIKADVVAAFAEEEDEEDEKEIKDIFKAL 60 Query: 299 QAKVVRTVMLDKKVRMDGRD 318 + KVVR+ +LD R+DGRD Sbjct: 61 EKKVVRSRILDGGPRIDGRD 80 >gnl|CDD|88463 cd05708, S1_Rrp5_repeat_sc12, S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.. Length = 77 Score = 51.4 bits (123), Expect = 8e-07 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 2/73 (2%) Query: 618 EVNKIYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTERVAKTSDVVKEGDTVWVKLLD 676 +V + G V +V D+G F+ G GL H S++S RVA S + + GD V K+L Sbjct: 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLK 60 Query: 677 FD-DRGKIKLSMK 688 D ++ +I L +K Sbjct: 61 IDAEKKRISLGLK 73 >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 = 51.4 bits (124), Expect = 8e-07 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 3/65 (4%) Query: 147 GPVVGAQVDYINGQYVLNPRLDED---QGSLDLFVSGTQDAVLMVELEANQLSEDVVLDA 203 GPV V I+G+ VL+P L+E+ L + V+GT D V +++ L+E+ +L+A Sbjct: 1 GPVAAVTVGKIDGELVLDPTLEEESLADSDLTIVVAGTGDIVALMKEGGGGLTEEELLEA 60 Query: 204 IIFGH 208 + H Sbjct: 61 LELAH 65 Score = 42.6 bits (101), Expect = 3e-04 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 8/72 (11%) Query: 458 PVAGIAMGLVKDGDDFIILSDISGDEDHLGH--MDFKVAGTDSGITAMQMDMKIGGISEN 515 PVA + +G + + ++ D + +E+ L + VAGT + M+ GG++E Sbjct: 2 PVAAVTVGKI--DGELVL--DPTLEEESLADSDLTIVVAGTGDIVALMKEG--GGGLTEE 55 Query: 516 IMVMALQQAKRG 527 ++ AL+ A +G Sbjct: 56 ELLEALELAHKG 67 >gnl|CDD|36287 KOG1069, KOG1069, KOG1069, Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis]. Length = 217 Score = 51.5 bits (123), Expect = 8e-07 Identities = 52/229 (22%), Positives = 91/229 (39%), Gaps = 24/229 (10%) Query: 319 SETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLSGTQRNDFMMHY 378 +E +R I+ ++ +L R GSS F +GDT+ I V G + R + Sbjct: 2 AERLRGIACEISILSRPDGSSEFSQGDTKVICSVY-GPID---------VKARQED---- 47 Query: 379 NFLPCATGEVS---RMGAPSRREIGHGRLARRAIHPVLPQTAQFPYTL-RIVSEITESDG 434 AT EV + G E R+ R+ + + +P T ++ ++ E DG Sbjct: 48 --PEKATLEVIWRPKSGVNGTVEKVLERIIRKTLSKAIILEL-YPRTTIQVSIQVVEDDG 104 Query: 435 SSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDE-DHLGHMDFKV 493 S+ + + LAL+DAG+P+ I+ L +DG ++L + E Sbjct: 105 STLACAINAACLALVDAGIPLRSMFCAISCALHEDGV--LVLDPTAKQEKISTARATLSF 162 Query: 494 AGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSES 542 G G + + G SE+ + L+ A+ + +VL Sbjct: 163 EGGSLGEPKVIISETNGEKSEDQLFYVLELAQAAAQSLFPFYREVLQRK 211 >gnl|CDD|32306 COG2123, COG2123, RNase PH-related exoribonuclease [Translation, ribosomal structure and biogenesis]. Length = 272 Score = 49.5 bits (118), Expect = 3e-06 Identities = 46/264 (17%), Positives = 96/264 (36%), Gaps = 40/264 (15%) Query: 308 LDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVVVTLGTREDEQYVDSLS 367 L K +R+DGR + R + + G++ + +GS+L G+TQ +V V E + D+ Sbjct: 19 LKKGIRIDGRSFDEFRPLEIETGVIPKANGSALVKLGNTQVVVGVKAEI--GEPFPDT-- 74 Query: 368 GTQRNDFMMHYNFLPCATGEVSRMGAPSRREIGHGRLARRAIHPVL--------PQTAQF 419 +++ P A G P I R+ R + + + Sbjct: 75 -PNEGVLVVNVELSPLA-SPSFEPGPPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKK 132 Query: 420 PYTLRIVSEITESDGSSSMATVCGSSLALMDAGVP----------------------ISK 457 + + + + + DG+ A + AL++ VP +S Sbjct: 133 VWVVFVDVHVLDYDGNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSN 192 Query: 458 PVAGIAMGLVKDGDDFIILSDISGDEDHLGHMDFKVAGTDSGITAMQMDMKIGGISENIM 517 P + + + +++ D S +E+ + + + G + G I+E+ + Sbjct: 193 PPISVTFAKIGN----VLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDL 248 Query: 518 VMALQQAKRGRLHILNEMSKVLSE 541 AL+ A + + + L E Sbjct: 249 EKALKTALSKAEKLREALKEALKE 272 Score = 40.7 bits (95), Expect = 0.002 Identities = 52/249 (20%), Positives = 97/249 (38%), Gaps = 50/249 (20%) Query: 14 RPLKLETGRIARQSDGAVLATYGETVVLATVV--YDRSLKDGQDFFPLTVNYQERTYAVG 71 RPL++ETG I + ++G+ L G T V+ V D + L VN + A Sbjct: 34 RPLEIETGVIPK-ANGSALVKLGNTQVVVGVKAEIGEPFPDTPNEGVLVVNVELSPLASP 92 Query: 72 KIPGGYLRRESRPTENEILISRMIDRSIRP------------LFSKCYKNETQVIINVMQ 119 G P E I +SR++DR +R K + V ++V+ Sbjct: 93 SFEPG------PPDELAIELSRVVDRGLRESKAIDLEKLCIEEGKKVWV--VFVDVHVLD 144 Query: 120 HDLESSPHVVSMVAASAALMLSGLP----------------------FEGPVVGAQVDYI 157 +D + + +AA AAL+ + +P P + I Sbjct: 145 YD--GNLIDAASLAAVAALLNTRVPKAVEVGDGEIVIEVEEEPVPLPVSNPPISVTFAKI 202 Query: 158 NGQYVLNPRLDED---QGSLDLFVSGTQDAVLMVELEANQLSEDVVLDAIIFGHNECKPV 214 V++P L+E+ G L + V+ + V + ++ ++E + A+ ++ + + Sbjct: 203 GNVLVVDPSLEEELVADGRLTITVNEDGEIVAIQKVGGGSITESDLEKALKTALSKAEKL 262 Query: 215 IEAISKLAK 223 EA+ + K Sbjct: 263 REALKEALK 271 >gnl|CDD|29002 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.. Length = 64 Score = 47.1 bits (112), Expect = 2e-05 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 7/64 (10%) Query: 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD------DGTVKIASSSLAEIEAA 606 E + +P + +IG GG I+ I E+TGAK+ I D + V I + + +E A Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTI-TGTPEAVEKA 59 Query: 607 REMI 610 +E+I Sbjct: 60 KELI 63 >gnl|CDD|88445 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 69 Score = 46.4 bits (110), Expect = 2e-05 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%) Query: 624 KGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLLDFD-DRG 681 G++ + DFG FV G DGLVHIS +S T+RV S++ K+G V +L+ D +R Sbjct: 5 SGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERE 64 Query: 682 KIKL 685 +I L Sbjct: 65 RISL 68 >gnl|CDD|88438 cd04473, S1_RecJ_like, S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.. Length = 77 Score = 45.1 bits (107), Expect = 6e-05 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 9/75 (12%) Query: 612 SITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVW 671 ++ D+ EV K+YKG+V V +G FV GL+H S L + + GD V Sbjct: 10 TMEDL-EVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRD--------YEVGDEVI 60 Query: 672 VKLLDFDDRGKIKLS 686 V++ D + G I L Sbjct: 61 VQVTDIPENGNIDLI 75 >gnl|CDD|88453 cd05698, S1_Rrp5_repeat_hs6_sc5, S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.. Length = 70 Score = 44.8 bits (106), Expect = 8e-05 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%) Query: 625 GQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-DRGKI 683 G +VKV G V F G + S+LS + + + G V VK+L D ++ ++ Sbjct: 6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRL 65 Query: 684 KLSMK 688 LS K Sbjct: 66 LLSCK 70 >gnl|CDD|88442 cd05687, S1_RPS1_repeat_ec1_hs1, S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 70 Score = 44.4 bits (105), Expect = 1e-04 Identities = 24/68 (35%), Positives = 34/68 (50%), Gaps = 1/68 (1%) Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDR- 680 I KG VV V D V +G++ IS+ S + + D VK GD V V +L +D Sbjct: 3 IVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEE 62 Query: 681 GKIKLSMK 688 G + LS + Sbjct: 63 GNVVLSKR 70 >gnl|CDD|88426 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.. Length = 99 Score = 43.3 bits (102), Expect = 2e-04 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 18/84 (21%) Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA-----------KTSDVVKEGDTV 670 + +G+VV+V+DFGAFV G DGL+HISQ+ + ++ +T V+K GD V Sbjct: 2 VVEGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVV 60 Query: 671 WVKL--LDFDDR----GKIKLSMK 688 ++ + +R KI L+M+ Sbjct: 61 RARIVAVSLKERRPRESKIGLTMR 84 >gnl|CDD|36288 KOG1070, KOG1070, KOG1070, rRNA processing protein Rrp5 [RNA processing and modification]. Length = 1710 Score = 43.1 bits (101), Expect = 3e-04 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 1/73 (1%) Query: 620 NKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDD 679 KI KG + + + GAFV F G G +S++S + V S+ G TV K+++ DD Sbjct: 600 GKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDD 659 Query: 680 -RGKIKLSMKVVD 691 + ++ L ++ Sbjct: 660 EKRRMPLGLRASS 672 >gnl|CDD|38127 KOG2916, KOG2916, KOG2916, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]. Length = 304 Score = 42.2 bits (99), Expect = 4e-04 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 3/80 (3%) Query: 617 PEVNKIYKGQVVKVMDFGAFVHFC--GARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674 PEV +I V + + GA+V +G++ +S+LS R+ +++ G V + Sbjct: 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVV 73 Query: 675 LDFD-DRGKIKLSMKVVDQN 693 L D ++G I LS + V Sbjct: 74 LRVDKEKGYIDLSKRRVSPE 93 >gnl|CDD|88444 cd05689, S1_RPS1_repeat_ec4, S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 72 Score = 41.2 bits (96), Expect = 0.001 Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 3/71 (4%) Query: 617 PEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLS-TERVAKTSDVVKEGDTVWVKLL 675 PE +++ G+V + D+G FV +GLVH+S++ T + S VV GD V V +L Sbjct: 2 PEGTRLF-GKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVL 60 Query: 676 DFD-DRGKIKL 685 D D +R +I L Sbjct: 61 DIDEERRRISL 71 >gnl|CDD|36889 KOG1676, KOG1676, KOG1676, K-homology type RNA binding proteins [RNA processing and modification]. Length = 600 Score = 40.0 bits (93), Expect = 0.002 Identities = 32/134 (23%), Positives = 61/134 (45%), Gaps = 26/134 (19%) Query: 492 KVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLG--EF 549 ++A SGI + + G EN+ + AK ++ E V+S R G + Sbjct: 88 QIAADPSGIG--YRSVDLTGSPENV-----EVAK----QLIGE---VVSRGRPPGGFPDN 133 Query: 550 TPRVEI---MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASS-------S 599 VE + IP ++ +IG GG+ I+ + EQ+G K+ + DG++ + Sbjct: 134 QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD 193 Query: 600 LAEIEAAREMIRSI 613 ++E A++++ I Sbjct: 194 PDKVEQAKQLVADI 207 Score = 38.9 bits (90), Expect = 0.005 Identities = 45/192 (23%), Positives = 75/192 (39%), Gaps = 32/192 (16%) Query: 431 ESDGSSSMATVCGSSLALMDAGVPISKPVAGIAMGLVKDGDDFIILSDISGDEDHLGHMD 490 E GS A V G A + VP SK GI +G K G+ L + +G + + Sbjct: 214 EVPGSGGHAGVRGGGSATREVKVPRSK--VGIIIG--KGGEMIKKLQNETGAK-----IQ 264 Query: 491 FKVAGTDSGITAMQMDMKIGGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFT 550 FK D ++ + +I G + I A ++NE+ Sbjct: 265 FK---PDDDPSSPERPAQIIGTVDQIEHAA---------ELINEIIAEAEAGAGGGMGGG 312 Query: 551 PRVEI----MAIPPDQIRNVIGMGGKVIRGIVEQTGAKV-------NIDDDGTVKIASSS 599 + M +P D+ VIG GG+ I+ I +Q+GA+ N + + Sbjct: 313 APGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGD 372 Query: 600 LAEIEAAREMIR 611 +I+ A+++IR Sbjct: 373 KRQIDHAKQLIR 384 Score = 32.3 bits (73), Expect = 0.49 Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 10/91 (10%) Query: 550 TPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREM 609 T + E +P + + VIG GG I+ I +++G +V I D S + Sbjct: 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAAD------PSGIGY---RSVD 102 Query: 610 IRSITDVPEVNKIYKGQVV-KVMDFGAFVHF 639 + + EV K G+VV + G F Sbjct: 103 LTGSPENVEVAKQLIGEVVSRGRPPGGFPDN 133 >gnl|CDD|31292 COG1095, RPB7, DNA-directed RNA polymerase, subunit E' [Transcription]. Length = 183 Score = 39.8 bits (93), Expect = 0.003 Identities = 30/95 (31%), Positives = 50/95 (52%), Gaps = 18/95 (18%) Query: 611 RSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVA-----------K 659 R++ P ++ +G+VV+V++FGAFV G DGLVH+SQ+ + + + Sbjct: 73 RALVFKPFRGEVVEGEVVEVVEFGAFVRI-GPLDGLVHVSQIMDDYIDYDEKNKVLIGEE 131 Query: 660 TSDVVKEGDTVWVKL--LDFDDRG----KIKLSMK 688 T V+K GD V ++ + R KI L+M+ Sbjct: 132 TKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMR 166 >gnl|CDD|29004 cd02394, vigilin_like_KH, K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.. Length = 62 Score = 39.4 bits (92), Expect = 0.003 Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 5/63 (7%) Query: 553 VEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNI----DDDGTVKIASSSLAEIEAARE 608 E + IP R +IG G IR I+E+TG K+ T+ I + +E A+E Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITI-TGPKENVEKAKE 59 Query: 609 MIR 611 I Sbjct: 60 EIL 62 >gnl|CDD|30903 COG0557, VacB, Exoribonuclease R [Transcription]. Length = 706 Score = 39.2 bits (91), Expect = 0.004 Identities = 26/82 (31%), Positives = 34/82 (41%), Gaps = 13/82 (15%) Query: 619 VNKIYKGQVVKVMDFGAFVHFCG-ARDGLVHISQLSTE-----------RVAKTSDVVKE 666 V + + G V V FG FV +GLVHIS L + K+ V + Sbjct: 622 VGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRL 681 Query: 667 GDTVWVKLLDFD-DRGKIKLSM 687 GD V VK+ D D KI + Sbjct: 682 GDEVKVKVTSVDLDERKIDFEL 703 >gnl|CDD|31291 COG1094, COG1094, Predicted RNA-binding protein (contains KH domains) [General function prediction only]. Length = 194 Score = 37.5 bits (87), Expect = 0.011 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 5/73 (6%) Query: 547 GEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNID-DDGTVKIASSSLAE--- 602 E + IP D+I +IG G+V + I E+TG K+ ID G+V I ++ E Sbjct: 3 EFAEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPL 62 Query: 603 -IEAAREMIRSIT 614 + AR+++++I Sbjct: 63 ALLKARDVVKAIG 75 >gnl|CDD|37401 KOG2190, KOG2190, KOG2190, PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification, General function prediction only]. Length = 485 Score = 37.4 bits (86), Expect = 0.012 Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 1/42 (2%) Query: 550 TPRVEI-MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD 590 P V + +P Q+ ++IG GG +I+ I E+TGAK+ + D Sbjct: 135 GPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD 176 Score = 30.1 bits (67), Expect = 2.0 Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 9/65 (13%) Query: 556 MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNI--------DDDGTVKIASSSLAEIEAAR 607 + +P D I +IG GG I I ++TGA ++I + V+I + L E A+ Sbjct: 342 LLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVREALVQI-TGMLREDLLAQ 400 Query: 608 EMIRS 612 +IR+ Sbjct: 401 YLIRA 405 >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 = 37.5 bits (87), Expect = 0.013 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%) Query: 617 PEVNKIYKGQVVKVMDF--GAFVHFCGARDGLVHISQLSTE---RVAKTSDVVKEGDTVW 671 P V IY G+V K++ AFV ++G +H+S + + K + ++KEG + Sbjct: 5 PIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEIL 64 Query: 672 V 672 V Sbjct: 65 V 65 >gnl|CDD|88446 cd05691, S1_RPS1_repeat_ec6, S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 73 Score = 36.7 bits (85), Expect = 0.020 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 1/71 (1%) Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFDDRG 681 I G+V +V GA V +G + ++LS +RV ++ K GD V K+ + D + Sbjct: 3 IVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKN 62 Query: 682 -KIKLSMKVVD 691 KI LS+K + Sbjct: 63 RKISLSIKAKE 73 >gnl|CDD|29006 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.. Length = 65 Score = 35.1 bits (81), Expect = 0.063 Identities = 13/35 (37%), Positives = 21/35 (60%) Query: 556 MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDD 590 + +P Q ++IG GG I+ I E+TGAK+ + Sbjct: 4 LLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS 38 >gnl|CDD|48406 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.. Length = 61 Score = 33.6 bits (77), Expect = 0.21 Identities = 11/40 (27%), Positives = 21/40 (52%) Query: 548 EFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNI 587 + + + +P DQ+ IG GG+ +R + G K++I Sbjct: 21 DDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 >gnl|CDD|37928 KOG2717, KOG2717, KOG2717, Uncharacterized conserved protein with similarity to embryogenesis protein H beta 58 and VPS26 [General function prediction only]. Length = 313 Score = 33.4 bits (76), Expect = 0.23 Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 6/97 (6%) Query: 511 GISENIMVMALQQAKRGRLH--ILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNV-- 566 G+ NI + KRG LH + M ++ + L E P + I I PD +++ Sbjct: 112 GVFINIQYLLTCDIKRGYLHKPLTKTMEFIVESGPVDLPERPPEIVIFYITPDTLQHPLK 171 Query: 567 --IGMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLA 601 I G ++ G ++ T + G + + +S A Sbjct: 172 ERIKTPGFLVTGKLDATQCSLTDPLTGELTVEASEAA 208 >gnl|CDD|88436 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.. Length = 83 Score = 33.1 bits (76), Expect = 0.29 Identities = 24/82 (29%), Positives = 36/82 (43%), Gaps = 13/82 (15%) Query: 619 VNKIYKGQVVKVMDFGAFVHFCGAR-DGLVHISQLSTE-----------RVAKTSDVVKE 666 V + + G + V FG FV +GLVH+S L + +T V + Sbjct: 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRL 60 Query: 667 GDTVWVKLLDFD-DRGKIKLSM 687 GD V V+++ D DR KI + Sbjct: 61 GDKVKVRVVRVDLDRRKIDFEL 82 >gnl|CDD|36825 KOG1612, KOG1612, KOG1612, Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]. Length = 288 Score = 32.7 bits (74), Expect = 0.35 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 3/53 (5%) Query: 312 VRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVV---VTLGTREDEQ 361 +R DGR R I + +L T+GS+ GD I+V +G+ +DE Sbjct: 21 IRNDGRSCHQFRPIEVETDVLPGTNGSARVKLGDGTDIIVGVKAEVGSPDDET 73 >gnl|CDD|32040 COG1855, COG1855, ATPase (PilT family) [General function prediction only]. Length = 604 Score = 32.2 bits (73), Expect = 0.57 Identities = 33/167 (19%), Positives = 63/167 (37%), Gaps = 12/167 (7%) Query: 514 ENIMVMALQQA------KRGRLHILNEMSKVLSESRLQLGEFTPRVEIMAIPPDQIRNVI 567 E ++V+ +++ K I E+ + L +++ ++ +P I VI Sbjct: 443 EQVVVVPVKEEEESPALKLAEEEIEREIKRYLP-GDVEVEVVGDGRAVVKVPEKYIPKVI 501 Query: 568 GMGGKVIRGIVEQTGAKVNIDDDGTVKIASSSLAEIEAAREMIRSITDVPEVNKIYKGQV 627 G GGK I+ I ++ G K+++ + EIE + I K + Sbjct: 502 GKGGKRIKEIEKKLGIKIDVKPLEEEEEGEKVPVEIEEKGKHIVLYVGPDFAGKPVRIYA 561 Query: 628 VKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKL 674 F A V +R G+V I +E + + + G + L Sbjct: 562 GDEYLFTATV----SRKGVVKIR-KDSEVGKEIEEAIDNGRDIRASL 603 >gnl|CDD|30544 COG0195, NusA, Transcription elongation factor [Transcription]. Length = 190 Score = 31.7 bits (72), Expect = 0.68 Identities = 14/38 (36%), Positives = 24/38 (63%) Query: 552 RVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD 589 V I+ +PPDQ+ IG GG+ +R + TG +++I+ Sbjct: 142 HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 >gnl|CDD|88452 cd05697, S1_Rrp5_repeat_hs5, S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.. Length = 69 Score = 31.3 bits (71), Expect = 1.0 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 1/67 (1%) Query: 622 IYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDFD-DR 680 + KG + K+ G FV GLV L+ R+ K G V ++L + +R Sbjct: 3 VVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPER 62 Query: 681 GKIKLSM 687 ++ L++ Sbjct: 63 KRLVLTL 69 >gnl|CDD|36110 KOG0892, KOG0892, KOG0892, Protein kinase ATM/Tel1, involved in telomere length regulation and DNA repair [Signal transduction mechanisms, Chromatin structure and dynamics, Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning]. Length = 2806 Score = 30.8 bits (69), Expect = 1.2 Identities = 12/61 (19%), Positives = 26/61 (42%), Gaps = 1/61 (1%) Query: 272 KKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGL 331 K + + ++N ++ VR +M ++ ++DG + T+ + AQV Sbjct: 2726 LKALKKQKEEDEENFNLSGNITEDASNDRNAVRALMRAQR-KLDGVEQGTMLSVEAQVQE 2784 Query: 332 L 332 L Sbjct: 2785 L 2785 >gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]. Length = 715 Score = 30.7 bits (69), Expect = 1.3 Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 8/81 (9%) Query: 612 SITDVPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVW 671 ++ DV E K YKG V +V +G FV GL+H L + GD + Sbjct: 116 TMEDV-EAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGDP------DYAVGDEII 168 Query: 672 VKLLDF-DDRGKIKLSMKVVD 691 V++ D ++G+I +D Sbjct: 169 VQVSDVRPEKGEIDFEPVGLD 189 >gnl|CDD|34549 COG4941, COG4941, Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]. Length = 415 Score = 30.7 bits (69), Expect = 1.3 Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 8/64 (12%) Query: 403 RLARRAIHPVLPQTAQFPYTLRIVSEITESD-------GSSSMAT-VCGSSLALMDAGVP 454 RL HP LP + TLR+V ++ ++ ++MA + + + +AG+P Sbjct: 111 RLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKARIREAGIP 170 Query: 455 ISKP 458 P Sbjct: 171 FEVP 174 >gnl|CDD|32705 COG2878, COG2878, Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]. Length = 198 Score = 30.7 bits (69), Expect = 1.4 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%) Query: 209 NECKPVIEA-ISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVSC 256 N C P EA I K+A++ EP D + + + M +I E + C Sbjct: 72 NRCAPGGEAVIRKIAELLGVEPPPADGSEHGEEQARMVALIDEANCIGC 120 >gnl|CDD|36826 KOG1613, KOG1613, KOG1613, Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]. Length = 298 Score = 30.7 bits (69), Expect = 1.5 Identities = 18/67 (26%), Positives = 28/67 (41%) Query: 292 VSVFEDIQAKVVRTVMLDKKVRMDGRDSETVRDISAQVGLLQRTHGSSLFIRGDTQAIVV 351 VF+ I ++ L + +R DGR RD + G + +GS+L G T I Sbjct: 16 PEVFKRISPELYLQRHLSEGIRPDGRKLGEFRDTAINAGNISTANGSALLKSGKTTVICG 75 Query: 352 VTLGTRE 358 + E Sbjct: 76 IKAEIAE 82 >gnl|CDD|37490 KOG2279, KOG2279, KOG2279, Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]. Length = 608 Score = 30.5 bits (68), Expect = 1.8 Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 5/80 (6%) Query: 536 SKVLSESRLQLGEFTPRVEIMAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDDDGT--- 592 K + L E TP E +++P + +IG GG+ IR I + +GAK+ D +G Sbjct: 124 CKAKAAIHQILTENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGL 183 Query: 593 --VKIASSSLAEIEAAREMI 610 + S E+ AA+ +I Sbjct: 184 SRLIKISGQQKEVAAAKHLI 203 Score = 29.3 bits (65), Expect = 3.8 Identities = 24/118 (20%), Positives = 51/118 (43%), Gaps = 8/118 (6%) Query: 510 GGISENIMVMALQQAKRGRLHILNEMSKVLSESRLQLGEFTPRVEI---MAIPPDQIRNV 566 S + + ++ + + R Q E P+ +I M +P + ++ + Sbjct: 23 IPASATVAYILYRKYRNDEEERDSGGQLTFVGIRGQTEEQKPQKDIEIEMVVPQEAVKLI 82 Query: 567 IGMGGKVIRGIVEQTGAKVNIDD----DGTVKIASSSLAEIEAAR-EMIRSITDVPEV 619 IG G I+ + +QTGAK+++D D V + S ++ A+ + + +T+ V Sbjct: 83 IGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTENTPV 140 >gnl|CDD|36140 KOG0922, KOG0922, KOG0922, DEAH-box RNA helicase [RNA processing and modification]. Length = 674 Score = 30.2 bits (68), Expect = 1.9 Identities = 24/118 (20%), Positives = 38/118 (32%), Gaps = 10/118 (8%) Query: 589 DDGTVKIASSSLAEIEAAREMIRSIT-----DVPEVNKIYKGQVVKVMDFGAFV-HFCGA 642 G + + + EIEAA E++R D PE+ G + F G Sbjct: 257 PPGDILVFLTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGK 316 Query: 643 RD-GLVHISQLSTERVAKTSDVVKEGDTVWVKL---LDFDDRGKIKLSMKVVDQNTGK 696 R L ++ + VV G K D + +S +Q G+ Sbjct: 317 RKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKASANQRAGR 374 >gnl|CDD|88464 cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".. Length = 86 Score = 30.1 bits (68), Expect = 1.9 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 6/85 (7%) Query: 616 VPEVNKIYKGQVVKVMDFGAFVHFCGARDGLVHISQLSTERVAKT----SDVVKEGDTVW 671 +PEV + G+V +V V D ++ +S+++ R + + EGD + Sbjct: 3 IPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIV 62 Query: 672 VKLLDFDDRGKIKLSMKVVDQNTGK 696 ++ D G + L + GK Sbjct: 63 AEVQSVDSDGSVSLHTR--SLKYGK 85 >gnl|CDD|31293 COG1096, COG1096, Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]. Length = 188 Score = 29.9 bits (67), Expect = 2.8 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 10/89 (11%) Query: 602 EIEAAREMIRSITDVPEVNKIYKGQVVKVMDFGAFVHFCGARD----------GLVHISQ 651 + + + +P+ I G+V V + A V G +H+SQ Sbjct: 47 NRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQ 106 Query: 652 LSTERVAKTSDVVKEGDTVWVKLLDFDDR 680 + V K SD + GD V +++ D Sbjct: 107 VRDGYVEKLSDAFRIGDIVRARVISTGDP 135 >gnl|CDD|147130 pfam04816, DUF633, Family of unknown function (DUF633). This family of proteins are uncharacterized have no known function. Length = 204 Score = 29.6 bits (67), Expect = 3.0 Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 3/33 (9%) Query: 557 AIPPDQIRNVI---GMGGKVIRGIVEQTGAKVN 586 I + +VI GMGG +I I+EQ K+ Sbjct: 60 VIEELDLIDVIVIAGMGGTLIADILEQGKNKLA 92 >gnl|CDD|88451 cd05696, S1_Rrp5_repeat_hs4, S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.. Length = 71 Score = 29.4 bits (66), Expect = 3.3 Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%) Query: 626 QVVKVM-DFGAFVHFCGARDGLVHISQLSTERVAKTSDVVKEGDTVWVKLLDF 677 +V KV D GA G VHIS LS ++V + K G T +++ + Sbjct: 8 KVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGY 60 >gnl|CDD|32239 COG2056, COG2056, Predicted permease [General function prediction only]. Length = 444 Score = 29.4 bits (66), Expect = 3.5 Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 2/39 (5%) Query: 434 GSSSMATVC--GSSLALMDAGVPISKPVAGIAMGLVKDG 470 G S +AT+ G++ AL DAG P S G GL DG Sbjct: 375 GFSPLATIALIGTAAALGDAGSPASDSTLGPTSGLNADG 413 >gnl|CDD|38893 KOG3689, KOG3689, KOG3689, Cyclic nucleotide phosphodiesterase [Signal transduction mechanisms]. Length = 707 Score = 29.2 bits (65), Expect = 3.5 Identities = 27/136 (19%), Positives = 43/136 (31%), Gaps = 26/136 (19%) Query: 569 MGGKVIRGIVEQTGAKVNIDD-------DGTVKIASSSLAEIEA--AREMIRSITDVPEV 619 + +RG V TG +NI + D V + + I + + V ++ Sbjct: 243 LLDYGLRGYVASTGEGLNISNAIADPRFDKQVDEDGTGIRPILCIPIKNKKGEVIGVQQL 302 Query: 620 NKIYKGQVVKVMD---FGAFVHFCGARDGLVHISQLSTERVAK--------------TSD 662 G D F AF FCG H+ + + + Sbjct: 303 VNKEDGNPFSRNDEDLFEAFTIFCGLSIHNTHMYSKINKSEPRQGVALEFLSYHAKALEE 362 Query: 663 VVKEGDTVWVKLLDFD 678 V+ G +KLLDF Sbjct: 363 EVQWGPATILKLLDFF 378 >gnl|CDD|48083 cd03466, Nitrogenase_NifN_2, Nitrogenase_nifN_2: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). This group also contains the Clostidium fused NifN-NifB protein.. Length = 429 Score = 29.5 bits (66), Expect = 3.7 Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 5/68 (7%) Query: 195 LSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRV 254 + E+ ++ +I +E K + E + + K ++ +++D DF +E ++L++ Sbjct: 319 VLENGMVPVLIATGSESKKLKEKLEEDLKEYVEKCVILDGADFFDIESYA-----KELKI 373 Query: 255 SCFIPEKY 262 I Y Sbjct: 374 DVLIGNSY 381 >gnl|CDD|38225 KOG3015, KOG3015, KOG3015, F1-ATP synthase assembly protein [Energy production and conversion]. Length = 283 Score = 29.2 bits (65), Expect = 3.8 Identities = 11/68 (16%), Positives = 29/68 (42%), Gaps = 1/68 (1%) Query: 248 IKEDLRVSCFIPEKYVRCKQIDDLKKKMVSYFSSEHSSWNEGEIVSVFEDIQAKVVRTVM 307 + L V + + KQ + K+ + + SS + W + +++ V+ + Sbjct: 169 FENRLGVKLQPSDNILGGKQAEKDKEAIDKWLSS-LNFWALAGLEFAVASLKSFVIALGI 227 Query: 308 LDKKVRMD 315 ++ K+ +D Sbjct: 228 IEGKLDVD 235 >gnl|CDD|113841 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This family consists of REP proteins from Dictyostelium (Slime molds). REP protein is likely involved in transcription regulation and control of DNA replication, specifically amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity. Length = 910 Score = 29.0 bits (65), Expect = 4.4 Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 2/45 (4%) Query: 205 IFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIK 249 IFG N+ + VI S L ++ K I D FS++ +++ ++ K Sbjct: 389 IFGQNKSEKVITLSSSLFELANK--IDYDEIKFSEISDDVFELSK 431 >gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 589 Score = 29.1 bits (65), Expect = 4.4 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%) Query: 205 IFGHNECKPVIEAISKLAKMCAKEPIVIDSKDFSKLEEEMSQMIKEDLRVS 255 ++ PVIE + I +D K+E+EM ++ KE+L + Sbjct: 44 LYPDVTIGPVIEEGFYYDFDVKEP---ITPEDLLKIEKEMKEIAKENLPIE 91 >gnl|CDD|30316 cd02784, MopB_CT_PHLH, The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.. Length = 137 Score = 28.8 bits (64), Expect = 4.8 Identities = 18/73 (24%), Positives = 24/73 (32%), Gaps = 9/73 (12%) Query: 7 VEIEWAGRPLKLETGRIARQSDGAVLAT--YGETVVLATV------VYDRSLKDGQDF-F 57 V I GR ++L ++G VL YG T Y D DF Sbjct: 58 VRIRRGGRTIELPVWIQPGHAEGVVLLALGYGRTHAGKVGNGVGHNAYPFRTSDVPDFVA 117 Query: 58 PLTVNYQERTYAV 70 + V R Y + Sbjct: 118 GVEVTKTGRKYPL 130 >gnl|CDD|111045 pfam02106, Fanconi_C, Fanconi anaemia group C protein. Length = 559 Score = 29.1 bits (65), Expect = 4.9 Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 5/28 (17%) Query: 413 LPQTAQFPYTLRIVSEI-----TESDGS 435 LPQ A P RIV EI E+DG+ Sbjct: 282 LPQAACHPAIFRIVDEIFRNALLETDGA 309 >gnl|CDD|146704 pfam04204, HTS, Homoserine O-succinyltransferase. Length = 298 Score = 29.0 bits (66), Expect = 5.1 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 15/49 (30%) Query: 513 SENIMVMALQQAKRG-----RLHILNEMSK----------VLSESRLQL 546 SENI VM ++A R R+ ILN M K +L + LQ+ Sbjct: 16 SENIFVMDEERAARQDIRPLRIGILNLMPKKIETETQLLRLLGNTPLQV 64 >gnl|CDD|37403 KOG2192, KOG2192, KOG2192, PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification, General function prediction only]. Length = 390 Score = 28.5 bits (63), Expect = 6.2 Identities = 13/34 (38%), Positives = 22/34 (64%) Query: 556 MAIPPDQIRNVIGMGGKVIRGIVEQTGAKVNIDD 589 + IP D ++IG GG+ I+ I ++GA + ID+ Sbjct: 319 VTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE 352 >gnl|CDD|146056 pfam03233, Cauli_AT, Aphid transmission protein. This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus. This protein interacts with the PIII protein. Length = 163 Score = 28.2 bits (63), Expect = 7.3 Identities = 8/26 (30%), Positives = 13/26 (50%) Query: 260 EKYVRCKQIDDLKKKMVSYFSSEHSS 285 +K VR K ++ YFSS+ + Sbjct: 14 DKIVRLKPLELSSNDRSYYFSSQKGN 39 >gnl|CDD|173880 cd08515, PBP2_NikA_DppA_OppA_like_10, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 460 Score = 28.3 bits (64), Expect = 8.1 Identities = 7/22 (31%), Positives = 10/22 (45%) Query: 555 IMAIPPDQIRNVIGMGGKVIRG 576 I +PPDQ + G + G Sbjct: 216 ITNVPPDQAERLKSSPGLTVVG 237 >gnl|CDD|88574 cd05134, RasGAP_RASA3, RASA3 (or GAP1_IP4BP) is a member of the GAP1 family and has been shown to specifically bind 1,3,4,5-tetrakisphosphate (IP4). Thus, RASA3 may function as an IP4 receptor. The members of GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. Purified RASA3 stimulates GAP activity on Ras with about a five-fold lower potency than p120RasGAP, but shows no GAP-stimulating activity at all against Rac or Rab3A.. Length = 310 Score = 28.1 bits (62), Expect = 9.5 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 4/80 (5%) Query: 190 LEANQLSEDVVLDAIIFGHNECKPVIEAISKLAKMCAKEPIVI-DSKDFSKLEEEMSQMI 248 L + + E + L + + KP+I+ I + K C +P+ + D ++ E + Q + Sbjct: 78 LTSKCIDETMKLAGMHYLQVTLKPIIDEICQEHKPCEIDPVKLKDGENLENNRENLRQYV 137 Query: 249 KEDLRVSCFIPEKYVRCKQI 268 RV I + V C + Sbjct: 138 DRIFRV---ITKSGVSCPTV 154 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 0.319 0.135 0.380 Gapped Lambda K H 0.267 0.0631 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,111,522 Number of extensions: 436186 Number of successful extensions: 1273 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1225 Number of HSP's successfully gapped: 99 Length of query: 699 Length of database: 6,263,737 Length adjustment: 101 Effective length of query: 598 Effective length of database: 4,081,228 Effective search space: 2440574344 Effective search space used: 2440574344 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 (21.7 bits) S2: 61 (27.5 bits)