RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780151|ref|YP_003064564.1| tRNA-specific 2-thiouridylase MnmA [Candidatus Liberibacter asiaticus str. psy62] (408 letters) >gnl|CDD|178898 PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed. Length = 346 Score = 494 bits (1274), Expect = e-140 Identities = 173/365 (47%), Positives = 226/365 (61%), Gaps = 20/365 (5%) Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80 RVVV MSGGVDSSV AALLK GY+VIGV ++L++ KG CCA +D+ DARRV Sbjct: 1 KRVVVGMSGGVDSSVAAALLKEQGYEVIGVFMKLWDD-DDETGKGGCCAEEDIADARRVA 59 Query: 81 DTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGADV 140 D + + HYV D+E+ F + VI F Y AG TP PCV CN+ +KF L R+LGAD Sbjct: 60 DKLGIPHYVVDFEKEFWDRVIDYFLDEYKAGRTPNPCVLCNKEIKFKAFLEYARELGADY 119 Query: 141 LATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMKKESV 200 +ATGHY R R R + R +D +DQSYFL+ TQ+QL L FPLG++ K V Sbjct: 120 IATGHYARIR--------DGRELLRGVDPNKDQSYFLYQLTQEQLAKLLFPLGELTKPEV 171 Query: 201 RDLAREMGLDIADKSDSQDICFVQQGKYFDVVKRINAGIALEGDIVHLNGQILGRHNGII 260 R++A E GL +A K DSQ ICF+ + Y D +KR A G+IV L+G++LG H G++ Sbjct: 172 REIAEEAGLPVAKKKDSQGICFIGERDYRDFLKRYLP--AQPGEIVDLDGKVLGEHKGLM 229 Query: 261 NYTIGQRRGLGVA-MGEPLFVVYLDKNSSRVIVGPRESLEVHRIYLREINWLGDGLFEDA 319 YTIGQR+GLG+ GEP +VV D ++ V+VG E+L + ++NW+G E Sbjct: 230 YYTIGQRKGLGIGGDGEPWYVVGKDPETNTVVVGQGEALYSRELIASDLNWVGGEPPE-- 287 Query: 320 VVDGFKCFVKIRSSQDPVPVFVQRNDDGVYVDFEKSEVGVASGQACVFYTSDSNEARVLG 379 + F+C KIR Q PVP V+ DD V V+F++ + V GQA VFY D RVLG Sbjct: 288 --EPFECTAKIRYRQKPVPATVELEDDRVEVEFDEPQRAVTPGQAAVFYDGD----RVLG 341 Query: 380 GGIIS 384 GGII Sbjct: 342 GGIIE 346 >gnl|CDD|161871 TIGR00420, trmU, tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase. tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU, asuE, or mnmA) is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in the wobble position of some tRNAs. This enzyme appears not to occur in the Archaea. Length = 352 Score = 313 bits (804), Expect = 5e-86 Identities = 135/368 (36%), Positives = 206/368 (55%), Gaps = 21/368 (5%) Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80 +V+V +SGGVDSSV A LLK+ GY+V+GV ++ + + G C + +D+ DA+ +C Sbjct: 1 KKVIVGLSGGVDSSVSAYLLKQQGYEVVGVFMKNWEEDDKNDGHG-CTSAEDLRDAQAIC 59 Query: 81 DTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQ-LGAD 139 + + + ++++ + N V PF Y G TP P + CN+ +KF L + LG D Sbjct: 60 EKLGIPLEKVNFQKEYWNKVFEPFIQEYKEGRTPNPDILCNKFIKFGAFLEYAAELLGND 119 Query: 140 VLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMKKES 199 +ATGHY R +GK + R +D +DQSYFL+ + +QL L FPLG++ K Sbjct: 120 KIATGHYARIA---EIEGKSL--LLRALDKNKDQSYFLYHLSHEQLAKLLFPLGELLKPE 174 Query: 200 VRDLAREMGLDIADKSDSQDICFVQQGKYFDVVKRINAGIALEGDIVHLNGQ-ILGRHNG 258 VR +A+ GL A+K DSQ ICF+ + K+ D +K+ G I+ ++GQ ++G H+G Sbjct: 175 VRQIAKNAGLPTAEKKDSQGICFIGERKFRDFLKKYLP--VKPGVIITVDGQSVIGEHDG 232 Query: 259 IINYTIGQRRGLGVAMG-EPLFVVYLDKNSSRVIVG-PRESLEVHRIYLREINWLGDGLF 316 + YTIGQR+GLG+ EP FVV D ++ +IV + L + ++ +WL D Sbjct: 233 LWFYTIGQRKGLGIGGAAEPWFVVEKDLETNELIVSHGKPDLASRGLLAQQFHWLDDEPN 292 Query: 317 EDAVVDGFKCFVKIRSSQDPVPVFVQRNDDGVY-VDFEKSEVGVASGQACVFYTSDSNEA 375 + +C VKIR Q PV ++ DD + V F++ + GV GQ+ V Y D Sbjct: 293 PFEM----RCTVKIRYRQVPVQCKLKLLDDNLIEVIFDEPQAGVTPGQSAVLYKGD---- 344 Query: 376 RVLGGGII 383 LGGGII Sbjct: 345 ICLGGGII 352 >gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA; Provisional. Length = 362 Score = 194 bits (493), Expect = 5e-50 Identities = 127/389 (32%), Positives = 193/389 (49%), Gaps = 59/389 (15%) Query: 17 NPKDMRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDA 76 RV+V MSGG+DS+ +L+ GY+++GVT++++ G + DA Sbjct: 2 KESKKRVLVGMSGGIDSTATCLMLQEQGYEIVGVTMRVW--------------GDEPQDA 47 Query: 77 RRVCDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQL 136 R + + + HYV D F++ ++ F Y G TP PCV CN KF L+ +L Sbjct: 48 RELAARMGIEHYVADERVPFKDTIVKNFIDEYRQGRTPNPCVMCNPLFKFRMLIEWADKL 107 Query: 137 GADVLATGHYIR-----SRLYV--GDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLR 189 G +ATGHY R +Y+ GDD K +DQSYFL+ Q L Sbjct: 108 GCAWIATGHYSRLEERNGHIYIVAGDDDK------------KDQSYFLWRLGQDILRRCI 155 Query: 190 FPLGDMKKESVRDLAREMGLDIADKS-DSQDICFVQQGKYFDVVKRINAGIALE---GDI 245 FPLG+ K++VR+ RE G + K +S ++CF+ +G Y D ++ + E G Sbjct: 156 FPLGNYTKQTVREYLREKGYEAKSKEGESMEVCFI-KGDYRDFLREQCPELDTEVGPGWF 214 Query: 246 VHLNGQILGRHNGIINYTIGQRRGLGVAMGEPLFVVYLDKNSSRVIVGPRESLEVHRIYL 305 V+ G LG+H G YTIGQR+GL +A+G+P +V+ ++ + V++G E L+ + Sbjct: 215 VNSEGVKLGQHKGFPYYTIGQRKGLEIALGKPAYVLKINPQKNTVMLGDAEQLKAEYMLA 274 Query: 306 REINWLGDGLFEDAVVDG---FKC---FVKIRSSQDPVPVFVQRNDDG-VYVDFEKSEVG 358 +D +VD F C V+IR P+P V+R +DG + V F Sbjct: 275 E----------QDNIVDEQELFACPDLAVRIRYRSRPIPCRVKRLEDGRLLVRFLAEASA 324 Query: 359 VASGQACVFYTSDSNEARVLGGGIISGSK 387 +A GQ+ VFY RVLGG I+ + Sbjct: 325 IAPGQSAVFYEG----RRVLGGAFIASQR 349 >gnl|CDD|173128 PRK14665, mnmA, tRNA-specific 2-thiouridylase MnmA; Provisional. Length = 360 Score = 181 bits (460), Expect = 4e-46 Identities = 113/380 (29%), Positives = 183/380 (48%), Gaps = 40/380 (10%) Query: 19 KDMRVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARR 78 K+ RV++ MSGG DSSV A LL GY+V GVT + Y +++ + DAR Sbjct: 4 KNKRVLLGMSGGTDSSVAAMLLLEAGYEVTGVTFRFYEFNGSTEY---------LEDARA 54 Query: 79 VCDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGA 138 + + + + H +D + FR +I F Y +G TP+PC CN +K+ L + ++G Sbjct: 55 LAERLGIGHITYDARKVFRKQIIDYFIDEYMSGHTPVPCTLCNNYLKWPLLAKIADEMGI 114 Query: 139 DVLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMKKE 198 LATGHY+R + G+ + D+++DQS+FL+ Q+ L + P+G M K Sbjct: 115 FYLATGHYVRKQWIDGN-----YYITPAEDVDKDQSFFLWGLRQEILQRMLLPMGGMTKS 169 Query: 199 SVRDLAREMG-LDIADKSDSQDICFVQQGKYFDVVK-----------RINAGIALEGDIV 246 R A E G +A K DS +CF Y +K R G + Sbjct: 170 EARAYAAERGFEKVAKKRDSLGVCFCPM-DYRSFLKKCLCDESGDKNRNIYRKVERGRFL 228 Query: 247 HLNGQILGRHNGIINYTIGQRRGLGVAMGEPLFVVYLDKNSSRVIVGPRESLEVHRIYLR 306 +G + H G YTIGQRRGLG+ + +FV + ++ V++ ++LE ++L+ Sbjct: 229 DESGNFIAWHEGYPFYTIGQRRGLGIQLNRAVFVKEIHPETNEVVLASLKALEKTEMWLK 288 Query: 307 EINWLGDGLF---EDAVVDGFKCFVKIRSSQDPVPVFVQRNDDGVYVDFEKSEVGVASGQ 363 + N + + +D +V ++ R ++ V + D+ ++V + +A GQ Sbjct: 289 DWNIVNESRLLGCDDIIVK-----IRYRKQENHCTVTITP-DNLLHVQLHEPLTAIAEGQ 342 Query: 364 ACVFYTSDSNEARVLGGGII 383 A FY +LGGGII Sbjct: 343 AAAFYKDGL----LLGGGII 358 >gnl|CDD|184435 PRK13980, PRK13980, NAD synthetase; Provisional. Length = 265 Score = 47.1 bits (113), Expect = 7e-06 Identities = 53/219 (24%), Positives = 84/219 (38%), Gaps = 80/219 (36%) Query: 22 RVVVAMSGGVDSSVVAALLKRD-GYD-VIGVTLQLYNSRKASKRKGSCCAGQDVYDARRV 79 VV+ +SGG+DS+VVA L + G + V+ + + S D+ DA V Sbjct: 32 GVVLGLSGGIDSAVVAYLAVKALGKENVLALLMPSSVSPPE-----------DLEDAELV 80 Query: 80 CDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSV------T 133 + + + + V + I P ++ + + +D L V T Sbjct: 81 AEDLGIEYKVIE---------ITPIVDAFFS------------AIPDADRLRVGNIMART 119 Query: 134 R---------QLGADVLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQ-- 182 R + VL TG+ +S L +G YF T+ Sbjct: 120 RMVLLYDYANRENRLVLGTGN--KSELLLG--------------------YF----TKYG 153 Query: 183 QQLCDLRFPLGDMKKESVRDLAREMGL--DIADKSDSQD 219 DL P+GD+ K VR+LAR +G+ DI +K S D Sbjct: 154 DGAVDLN-PIGDLYKTQVRELARHLGVPEDIIEKPPSAD 191 >gnl|CDD|129369 TIGR00268, TIGR00268, conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server. Length = 252 Score = 47.1 bits (112), Expect = 8e-06 Identities = 46/195 (23%), Positives = 79/195 (40%), Gaps = 47/195 (24%) Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81 +V++A SGGVDSS++AA+ G +V+ +T+ S S R ++ DA + Sbjct: 14 KVLIAYSGGVDSSLLAAVCSDAGTEVLAITVV---SPSISPR--------ELEDAIIIAK 62 Query: 82 TINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGADVL 141 I V+H ++ +I PF ++ C C + V S L+ + G DV+ Sbjct: 63 EIGVNHEFVKIDK-----MINPFRAN-----VEERCYFCKKMV-LSILVKEAEKRGYDVV 111 Query: 142 ATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQLCDLRFPLGDMK--KES 199 G DD R R + E + P + K+ Sbjct: 112 VDGTN-------ADDLFDHRPGYRAVK-EF---------------NGVSPWAEFGITKKE 148 Query: 200 VRDLAREMGLDIADK 214 +R++A+ +G+ DK Sbjct: 149 IREIAKSLGISFPDK 163 >gnl|CDD|148238 pfam06508, ExsB, ExsB. This family includes putative transcriptional regulators from Bacteria and Archaea. Length = 137 Score = 45.3 bits (108), Expect = 3e-05 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 11/70 (15%) Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81 + VV +SGG+DS+ A K++GY+V +T Y R + + + A+++ Sbjct: 1 KAVVLLSGGLDSTTCLAWAKKEGYEVYALTFD-YGQRHSKELEC----------AKKIAK 49 Query: 82 TINVSHYVFD 91 + V H + D Sbjct: 50 ALGVEHKIVD 59 >gnl|CDD|178842 PRK00074, guaA, GMP synthase; Reviewed. Length = 511 Score = 45.0 bits (108), Expect = 4e-05 Identities = 13/24 (54%), Positives = 18/24 (75%) Query: 19 KDMRVVVAMSGGVDSSVVAALLKR 42 D +V++ +SGGVDSSV A LL + Sbjct: 214 GDKKVILGLSGGVDSSVAAVLLHK 237 >gnl|CDD|184346 PRK13820, PRK13820, argininosuccinate synthase; Provisional. Length = 394 Score = 43.4 bits (103), Expect = 1e-04 Identities = 29/88 (32%), Positives = 41/88 (46%), Gaps = 20/88 (22%) Query: 21 MRVVVAMSGGVDSSVVAALLK-RDGYD-VIGVTLQLYNSRKASKRKGSCCAGQ---DVYD 75 +VV+A SGG+D+SV LLK + GYD VI VT+ + GQ ++ + Sbjct: 3 KKVVLAYSGGLDTSVCVPLLKEKYGYDEVITVTVDV---------------GQPEEEIKE 47 Query: 76 ARRVCDTINVSHYVFDYEERFRNAVIVP 103 A + HY D +E F I P Sbjct: 48 AEEKAKKLGDKHYTIDAKEEFAKDYIFP 75 >gnl|CDD|129461 TIGR00364, TIGR00364, exsB protein. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown. Length = 201 Score = 42.8 bits (101), Expect = 2e-04 Identities = 32/128 (25%), Positives = 55/128 (42%), Gaps = 18/128 (14%) Query: 24 VVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCDTI 83 VV +SGG DS+ A+ K +GY+V +T Y R +++ AR++ + + Sbjct: 2 VVVLSGGQDSTTCLAIAKDEGYEVHAITFD-YGQR----------HSRELESARKIAEAL 50 Query: 84 NVSHYVFDY---EERFRNAV----IVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTRQL 136 + H+V D ++ +A+ +P S P V + S S L Sbjct: 51 GIEHHVIDLSLLKQLGGSALTDESEIPPQKSNEEDTLPNTFVPGRNAIFLSIAASYAEAL 110 Query: 137 GADVLATG 144 GA+ + TG Sbjct: 111 GAEAVITG 118 >gnl|CDD|161924 TIGR00552, nadE, NAD+ synthetase. NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of the family, such as from Mycobacterium tuberculosis, are considerably longer, contain an apparent amidotransferase domain, and show glutamine-dependent as well as NH(3)-dependent activity. Length = 250 Score = 39.7 bits (93), Expect = 0.001 Identities = 47/195 (24%), Positives = 73/195 (37%), Gaps = 54/195 (27%) Query: 23 VVVAMSGGVDSSVVAALLKRD-GYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81 VV+ +SGG+DS+VVAAL G + L + QDV DA + + Sbjct: 25 VVLGLSGGIDSAVVAALCVEALGEQNHALLLPHSVQ--TPE--------QDVQDALALAE 74 Query: 82 TINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVD-------CNRTVKFSDLLSVTR 134 + +++ D AS A ET D R + + L ++ Sbjct: 75 PLGINYKNIDIA--------PIAASFQAQTETGDELSDFLAKGNLKARL-RMAALYAIAN 125 Query: 135 QLGADVLATGHYIRSRLYVGDDGKRRRIMCRPMDLERDQSYFLFATTQQQL-CDLRFPLG 193 + VL TG+ +S L +G YF T CD+ P+G Sbjct: 126 KHNLLVLGTGN--KSELMLG--------------------YF---TKYGDGGCDIA-PIG 159 Query: 194 DMKKESVRDLAREMG 208 D+ K V +LA+ + Sbjct: 160 DLFKTQVYELAKRLN 174 >gnl|CDD|129143 TIGR00032, argG, argininosuccinate synthase. argG in bacteria, ARG1 in Saccharomyces cerevisiae. There is a very unusual clustering in the alignment, with a deep split between one cohort of E. coli, H. influenzae, and Streptomyces, and the other cohort of eukaryotes, archaea, and the rest of the eubacteria. Length = 394 Score = 39.7 bits (93), Expect = 0.002 Identities = 33/128 (25%), Positives = 51/128 (39%), Gaps = 20/128 (15%) Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQ--DVYDA--R 77 +VV+A SGG+D+SV L+ GY+VI T + GQ + DA Sbjct: 1 KVVLAYSGGLDTSVCLKWLREKGYEVIAYTADV---------------GQPEEDIDAIPE 45 Query: 78 RVCDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDC-NRTVKFSDLLSVTRQL 136 + + +HY D E F + A E P R + L+ ++ Sbjct: 46 KALEYGAENHYTIDAREEFVKDYGFAAIQANAFYEGTYPLSTALARPLIAKKLVEAAKKE 105 Query: 137 GADVLATG 144 GA+ +A G Sbjct: 106 GANAVAHG 113 >gnl|CDD|179859 PRK04527, PRK04527, argininosuccinate synthase; Provisional. Length = 400 Score = 39.0 bits (91), Expect = 0.002 Identities = 30/125 (24%), Positives = 45/125 (36%), Gaps = 14/125 (11%) Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVCD 81 +V+A SGG+D+S L+ GY V V G A + + +R + Sbjct: 4 DIVLAFSGGLDTSFCIPYLQERGYAVHTVFAD----------TGGVDAEERDFIEKRAAE 53 Query: 82 TINVSHYVFDYEERFRNAVIVPF--ASSYAAGETPLPCVDCNRTVKFSDLLSVTRQLGAD 139 SH D + P A G+ PL D R + L +LG Sbjct: 54 LGAASHVTVDGGPAIWEGFVKPLVWAGEGYQGQYPLLVSD--RYLIVDAALKRAEELGTR 111 Query: 140 VLATG 144 ++A G Sbjct: 112 IIAHG 116 >gnl|CDD|162088 TIGR00884, guaA_Cterm, GMP synthase (glutamine-hydrolyzing), C-terminal domain or B subunit. This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This C-terminal region would be the larger subunit. Length = 311 Score = 38.1 bits (89), Expect = 0.004 Identities = 14/24 (58%), Positives = 18/24 (75%) Query: 19 KDMRVVVAMSGGVDSSVVAALLKR 42 D +V++A+SGGVDSSV A L R Sbjct: 15 GDAKVIIALSGGVDSSVAAVLAHR 38 >gnl|CDD|162854 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). Length = 189 Score = 37.6 bits (88), Expect = 0.006 Identities = 25/131 (19%), Positives = 46/131 (35%), Gaps = 31/131 (23%) Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTLQL----YNSRKASKRKGSCCAGQDVYDAR 77 R++VA+SGGVDS + LL + + + L + R S +A Sbjct: 1 RILVAVSGGVDSMALLHLLLKL-QPKLKIRLIAAHVDHGLRPESDE-----------EAE 48 Query: 78 RV---CDTINVSHYVFDYEERFRNAVIVPFASSYAAGETPLPCVDCNRTVKFSDLLSVTR 134 V C +N+ + + + + A R ++ + + Sbjct: 49 FVQQFCKKLNIPLEIKKVDVKALA--KGKKKNLEEAA----------REARYDFFEEIAK 96 Query: 135 QLGADVLATGH 145 + GAD + T H Sbjct: 97 KHGADYILTAH 107 >gnl|CDD|179150 PRK00876, nadE, NAD synthetase; Reviewed. Length = 326 Score = 37.6 bits (88), Expect = 0.006 Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 13/71 (18%) Query: 23 VVVAMSGGVDSSVVAALLKRD-GYD-VIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80 VV+ +SGG+DSSV AAL R G + V G+ + +S S R G R V Sbjct: 36 VVLGLSGGIDSSVTAALCVRALGKERVYGLLMPERDSSPESLRLG-----------REVA 84 Query: 81 DTINVSHYVFD 91 + + V + V D Sbjct: 85 EHLGVEYVVED 95 >gnl|CDD|179167 PRK00919, PRK00919, GMP synthase subunit B; Validated. Length = 307 Score = 36.4 bits (85), Expect = 0.013 Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 4/37 (10%) Query: 13 DLDKNPKDMRVVVAMSGGVDSSVVAALLKRDGYDVIG 49 ++ + D + ++A+SGGVDSSV A L + IG Sbjct: 14 EIREEIGDGKAIIALSGGVDSSVAAVL----AHRAIG 46 Score = 27.6 bits (62), Expect = 6.3 Identities = 10/20 (50%), Positives = 15/20 (75%) Query: 191 PLGDMKKESVRDLAREMGLD 210 PL D+ K+ VR++AR +GL Sbjct: 159 PLRDLYKDEVREVARALGLP 178 >gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional. Length = 399 Score = 35.8 bits (84), Expect = 0.022 Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 1/35 (2%) Query: 21 MRVVVAMSGGVDSSVVAALLKRD-GYDVIGVTLQL 54 +VV+A SGG+D+SV+ LK G +VI T + Sbjct: 3 KKVVLAYSGGLDTSVIIKWLKETYGCEVIAFTADV 37 >gnl|CDD|185431 PTZ00077, PTZ00077, asparagine synthetase-like protein; Provisional. Length = 586 Score = 34.7 bits (80), Expect = 0.040 Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 9/73 (12%) Query: 25 VAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAG----QDVYDARRVC 80 + +SGG+DSS+VAA++ + + ++ S++ + S C G D+ AR+V Sbjct: 242 LFLSGGLDSSIVAAIVAK-----LIKNGEIDLSKRGMPKLHSFCIGLEGSPDLKAARKVA 296 Query: 81 DTINVSHYVFDYE 93 + + H+ F + Sbjct: 297 EYLGTEHHEFTFT 309 >gnl|CDD|179454 PRK02628, nadE, NAD synthetase; Reviewed. Length = 679 Score = 34.1 bits (79), Expect = 0.062 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 13/54 (24%) Query: 6 ATRLNSLDLDKNPKDMRVVVAMSGGVDSS---VVAA----LLKRDGYDVIGVTL 52 A RL + L K VV+ +SGG+DS+ +VAA L +++ T+ Sbjct: 353 AQRLRATGLKK------VVIGISGGLDSTHALLVAAKAMDRLGLPRKNILAYTM 400 >gnl|CDD|178164 PLN02549, PLN02549, asparagine synthase (glutamine-hydrolyzing). Length = 578 Score = 32.8 bits (75), Expect = 0.17 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 19/76 (25%) Query: 25 VAMSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKG----SCCAGQ----DVYDA 76 V +SGG+DSS+VA++ R KA+++ G S C G D+ A Sbjct: 230 VLLSGGLDSSLVASIAARH-----------LAETKAARQWGQQLHSFCVGLEGSPDLKAA 278 Query: 77 RRVCDTINVSHYVFDY 92 R V D + H+ F + Sbjct: 279 REVADYLGTVHHEFHF 294 >gnl|CDD|184745 PRK14561, PRK14561, hypothetical protein; Provisional. Length = 194 Score = 32.5 bits (75), Expect = 0.23 Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%) Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGVT 51 M+ V SGG DSS+ A LL+R YDV VT Sbjct: 1 MKAGVLFSGGKDSSLAAILLERF-YDVELVT 30 >gnl|CDD|178263 PLN02657, PLN02657, 3,8-divinyl protochlorophyllide a 8-vinyl reductase. Length = 390 Score = 31.7 bits (72), Expect = 0.33 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 12/88 (13%) Query: 3 VSEATRLNSLDLDKNPKDMRVVVAMSGG-VDSSVVAALLKRDGYDVIGVTLQLYNSRKAS 61 + A K PKD+ V+V + G + VV L++R GY+V+ V R+ S Sbjct: 43 RATAAAAAQSFRSKEPKDVTVLVVGATGYIGKFVVRELVRR-GYNVVAVA------REKS 95 Query: 62 K---RKGSCCAGQDVYDARRV-CDTINV 85 + G +++ A V D + Sbjct: 96 GIRGKNGKEDTKKELPGAEVVFGDVTDA 123 >gnl|CDD|162406 TIGR01536, asn_synth_AEB, asparagine synthase (glutamine-hydrolyzing). This model describes the glutamine-hydrolysing asparagine synthase. A poorly conserved C-terminal extension was removed from the model. Bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis. Long-branch members of the phylogenetic tree (which typically were also second or third candidate members from their genomes) were removed from the seed alignment and score below trusted cutoff. Length = 467 Score = 31.5 bits (72), Expect = 0.35 Identities = 13/23 (56%), Positives = 19/23 (82%) Query: 20 DMRVVVAMSGGVDSSVVAALLKR 42 D+ V V +SGG+DSS+VAA+ +R Sbjct: 253 DVPVGVLLSGGLDSSLVAAIARR 275 >gnl|CDD|163334 TIGR03573, WbuX, N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an invariable contextual association with homologs of the HisH and HisF proteins known as WbuY and WbuZ, respectively. These two proteins are believed to supply the enzyme with ammonium by hydrolysis of glutamine and delivery through an ammonium conduit. Length = 343 Score = 31.5 bits (72), Expect = 0.37 Identities = 11/31 (35%), Positives = 20/31 (64%), Gaps = 1/31 (3%) Query: 23 VVVAMSGGVDSSVVAALLKRD-GYDVIGVTL 52 ++ +SGG DS+ A +LK+ G + + VT+ Sbjct: 62 CIIGVSGGKDSTYQAHVLKKKLGLNPLLVTV 92 >gnl|CDD|169417 PRK08384, PRK08384, thiamine biosynthesis protein ThiI; Provisional. Length = 381 Score = 31.5 bits (71), Expect = 0.40 Identities = 14/29 (48%), Positives = 20/29 (68%) Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGV 50 +VV +SGG+DS V A L+ + G +VI V Sbjct: 182 KVVALLSGGIDSPVAAFLMMKRGVEVIPV 210 >gnl|CDD|185554 PTZ00323, PTZ00323, NAD+ synthase; Provisional. Length = 294 Score = 31.7 bits (72), Expect = 0.41 Identities = 11/19 (57%), Positives = 15/19 (78%) Query: 24 VVAMSGGVDSSVVAALLKR 42 V ++SGG+DS+VV AL R Sbjct: 50 VTSVSGGIDSAVVLALCAR 68 >gnl|CDD|184436 PRK13981, PRK13981, NAD synthetase; Provisional. Length = 540 Score = 30.5 bits (70), Expect = 0.79 Identities = 10/17 (58%), Positives = 16/17 (94%) Query: 23 VVVAMSGGVDSSVVAAL 39 VV+ +SGG+DS++VAA+ Sbjct: 283 VVLGLSGGIDSALVAAI 299 >gnl|CDD|163136 TIGR03104, trio_amidotrans, asparagine synthase family amidotransferase. Members of this protein family are closely related to several isoforms of asparagine synthetase (glutamine amidotransferase) and typically have been given this name in genome annotation to date. Each is part of a conserved three-gene cassette sparsely distributed across at least twenty different species known so far, including alpha, beta, and gamma Proteobacteria, Mycobacterium, and Prosthecochloris, which is a member of the Chlorobi. The other two members of the cassette are a probable protease and a member of the GNAT family of acetyltransferases. Length = 589 Score = 30.4 bits (69), Expect = 0.93 Identities = 13/27 (48%), Positives = 18/27 (66%) Query: 20 DMRVVVAMSGGVDSSVVAALLKRDGYD 46 D+ V V +SGG+DSS++ LL G D Sbjct: 260 DVPVGVLLSGGLDSSLIVGLLAEAGVD 286 >gnl|CDD|177981 PLN02347, PLN02347, GMP synthetase. Length = 536 Score = 30.4 bits (69), Expect = 0.94 Identities = 12/23 (52%), Positives = 17/23 (73%) Query: 20 DMRVVVAMSGGVDSSVVAALLKR 42 D V+ A+SGGVDS+V A L+ + Sbjct: 229 DEHVICALSGGVDSTVAATLVHK 251 >gnl|CDD|169396 PRK08349, PRK08349, hypothetical protein; Validated. Length = 198 Score = 29.7 bits (67), Expect = 1.3 Identities = 12/30 (40%), Positives = 17/30 (56%) Query: 21 MRVVVAMSGGVDSSVVAALLKRDGYDVIGV 50 M+ V +S G+DS V L+ R G +V V Sbjct: 1 MKAVALLSSGIDSPVAIYLMLRRGVEVYPV 30 >gnl|CDD|161829 TIGR00342, TIGR00342, thiazole biosynthesis/tRNA modification protein ThiI. The protein product of the thiI gene is required for the synthesis of the thiazole moiety in thiamine biosynthesis. It also acts in the generation of 4-thiouridine in tRNA, and may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis. Length = 371 Score = 28.9 bits (65), Expect = 2.2 Identities = 11/31 (35%), Positives = 19/31 (61%) Query: 22 RVVVAMSGGVDSSVVAALLKRDGYDVIGVTL 52 +V+ +SGG+DS V A ++ + G V+ V Sbjct: 174 KVLALLSGGIDSPVAAFMMMKRGCRVVAVHF 204 >gnl|CDD|181851 PRK09431, asnB, asparagine synthetase B; Provisional. Length = 554 Score = 28.7 bits (65), Expect = 3.1 Identities = 10/23 (43%), Positives = 18/23 (78%) Query: 20 DMRVVVAMSGGVDSSVVAALLKR 42 D+ V +SGG+DSS+++A+ K+ Sbjct: 227 DVPYGVLLSGGLDSSLISAIAKK 249 >gnl|CDD|183714 PRK12742, PRK12742, oxidoreductase; Provisional. Length = 237 Score = 28.6 bits (64), Expect = 3.4 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 6/57 (10%) Query: 197 KESVRDLAREMGLDIADKSDSQD----ICFVQQGKYFDVVKRINAGIALEGDIVHLN 249 K++ LA+E G A ++DS D I V++ D++ +NAGIA+ GD + L+ Sbjct: 41 KDAAERLAQETGAT-AVQTDSADRDAVIDVVRKSGALDILV-VNAGIAVFGDALELD 95 >gnl|CDD|177973 PLN02339, PLN02339, NAD+ synthase (glutamine-hydrolysing). Length = 700 Score = 28.5 bits (64), Expect = 3.7 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 14/54 (25%) Query: 27 MSGGVDSSVVAALLKRDGYDVIGVTLQLYNSRKASKRKGSCCAGQDVYDARRVC 80 +SGG DSS VAA+ +G QL + R+G Q DARR+ Sbjct: 355 LSGGADSSSVAAI--------VGSMCQLVV---KAIREGD---EQVKADARRIG 394 >gnl|CDD|163033 TIGR02823, oxido_YhdH, putative quinone oxidoreductase, YhdH/YhfP family. This model represents a subfamily of pfam00107 as defined by Pfam, a superfamily in which some members are zinc-binding medium-chain alcohol dehydrogenases while others are quinone oxidoreductases with no bound zinc. This subfamily includes proteins studied crystallographically for insight into function: YhdH from Escherichia coli and YhfP from Bacillus subtilis. Members bind NADPH or NAD, but not zinc. Length = 323 Score = 28.3 bits (64), Expect = 3.8 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%) Query: 17 NPKDMRVVV-AMSGGVDSSVVAALLKRDGYDVIGVT 51 P+D V+V +GGV S+ A+L + GY+V+ T Sbjct: 143 TPEDGPVLVTGATGGV-GSLAVAILSKLGYEVVAST 177 >gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional. Length = 404 Score = 28.2 bits (63), Expect = 4.6 Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 1/35 (2%) Query: 18 PKDMRVVVAMSGGVDSSVVAALLKRD-GYDVIGVT 51 K +VV+A SGG+D+SV+ L+ + G +V+ T Sbjct: 3 GKLNKVVLAYSGGLDTSVILKWLRENYGCEVVCFT 37 >gnl|CDD|182548 PRK10559, PRK10559, p-hydroxybenzoic acid efflux subunit AaeA; Provisional. Length = 310 Score = 27.8 bits (62), Expect = 5.5 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 10/50 (20%) Query: 157 GKRRRIMCRPMDLER-DQSYFLFATTQQQLCDLRFPLGDMKKESVRDLAR 205 G+R R+ + M E DQ+ + T QL K ++ RDLA+ Sbjct: 109 GRRNRLGVQAMSREEIDQANNVLQTVLHQLA---------KAQATRDLAK 149 >gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional. Length = 436 Score = 27.7 bits (62), Expect = 6.3 Identities = 10/19 (52%), Positives = 16/19 (84%) Query: 22 RVVVAMSGGVDSSVVAALL 40 +++VA SGG+DS+V+ LL Sbjct: 17 QILVAFSGGLDSTVLLHLL 35 >gnl|CDD|184135 PRK13551, PRK13551, agmatine deiminase; Provisional. Length = 362 Score = 27.6 bits (62), Expect = 6.3 Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 8/38 (21%) Query: 295 RESLEVHRIYLREINWLGDGLFEDAV---VDGFKCFVK 329 R+ L V ++ WL DG++ D VD CFV+ Sbjct: 190 RDYLGVEKVI-----WLPDGIYNDETDGHVDNVCCFVR 222 >gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional. Length = 446 Score = 27.4 bits (62), Expect = 6.8 Identities = 8/11 (72%), Positives = 10/11 (90%) Query: 376 RVLGGGIISGS 386 RVLGGG++ GS Sbjct: 71 RVLGGGLVPGS 81 >gnl|CDD|179487 PRK02866, PRK02866, cyanate hydratase; Validated. Length = 147 Score = 27.5 bits (62), Expect = 6.8 Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%) Query: 11 SLDLDK--NPKDMRVVVAMSG 29 LD+DK +PK RVV+ + G Sbjct: 119 KLDVDKVEDPKGDRVVITLDG 139 >gnl|CDD|162036 TIGR00784, citMHS, citrate transporter, CitMHS family. This family includes two characterized citrate/proton symporters from Bacillus subtilis. CitM transports citrate complexed to Mg2+, while the CitH apparently transports citrate without Mg2+. The family also includes uncharacterized transporters, including a third paralog in Bacillus subtilis. Length = 431 Score = 27.5 bits (61), Expect = 6.9 Identities = 11/23 (47%), Positives = 16/23 (69%) Query: 381 GIISGSKRSDAVEESLLSVIGDE 403 GI+SG+K DA+ SL+S+I Sbjct: 300 GILSGTKMVDAMAGSLVSIIPSS 322 >gnl|CDD|180043 PRK05370, PRK05370, argininosuccinate synthase; Validated. Length = 447 Score = 27.2 bits (61), Expect = 7.0 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 5/39 (12%) Query: 6 ATRLNSLDLDKNPKDMRVVVAMSGGVDSSVVAALLKRDG 44 +T L L P RV +A SGG+D+S +++ G Sbjct: 2 STILKHL-----PVGQRVGIAFSGGLDTSAALLWMRQKG 35 >gnl|CDD|132036 TIGR02991, ectoine_eutB, ectoine utilization protein EutB. Members of this protein family are EutB, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. Members of this family resemble threonine dehydratases. Length = 317 Score = 27.5 bits (61), Expect = 7.2 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%) Query: 14 LDKNPKDMRVVVAMSGGVDSSVVAALLK--RDGYDVIGVTLQLYNSRKASKRKG 65 +++ P V+V +SGG +S VA +K R VIGV+++ + KAS + G Sbjct: 162 VEQMPDLATVLVPLSGGGLASGVAMAVKAARPDTRVIGVSMERGAAMKASLQAG 215 >gnl|CDD|182130 PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional. Length = 343 Score = 27.3 bits (61), Expect = 7.6 Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%) Query: 201 RDLAREMGLDIADKSDSQDICFVQQGK-YFDVV 232 LAREMG D + D+ + K YFDV Sbjct: 207 LSLAREMGADKLVNPQNDDLDHYKAEKGYFDVS 239 >gnl|CDD|178010 PLN02384, PLN02384, ribose-5-phosphate isomerase. Length = 264 Score = 27.1 bits (60), Expect = 8.1 Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 4/38 (10%) Query: 180 TTQQQLCDLRFPLGDMKKESVRDLAREMGLDIADKSDS 217 T +Q L PL D+ V DLA +D AD+ D Sbjct: 88 KTHEQAVSLGIPLSDLDSHPVVDLA----IDGADEVDP 121 >gnl|CDD|183587 PRK12550, PRK12550, shikimate 5-dehydrogenase; Reviewed. Length = 272 Score = 26.8 bits (60), Expect = 9.3 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 18 PKDMRVVVAMSGGVDSSVVAAL 39 P D+ V + SGG+ +V AAL Sbjct: 120 PPDLVVALRGSGGMAKAVAAAL 141 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.322 0.139 0.407 Gapped Lambda K H 0.267 0.0731 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 6,671,369 Number of extensions: 442345 Number of successful extensions: 1037 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1008 Number of HSP's successfully gapped: 72 Length of query: 408 Length of database: 5,994,473 Length adjustment: 96 Effective length of query: 312 Effective length of database: 3,920,105 Effective search space: 1223072760 Effective search space used: 1223072760 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: 58 (26.1 bits)