RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780234|ref|YP_003064647.1| argininosuccinate synthase [Candidatus Liberibacter asiaticus str. psy62] (404 letters) >gnl|CDD|179051 PRK00509, PRK00509, argininosuccinate synthase; Provisional. Length = 399 Score = 723 bits (1868), Expect = 0.0 Identities = 245/400 (61%), Positives = 301/400 (75%), Gaps = 3/400 (0%) Query: 4 DVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKEVYV 63 KKVVLAYSGGLDTS+I+KWL+ G EVI F AD+GQGEEL+ +KA GA E+YV Sbjct: 1 MKKKVVLAYSGGLDTSVIIKWLKETYGCEVIAFTADVGQGEELEPIREKALKSGASEIYV 60 Query: 64 KDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGK 123 +DLR EFVRD+VFP RANALYEG Y LGTA+ARPLIAK LV+IA + GADA+AHG TGK Sbjct: 61 EDLREEFVRDYVFPAIRANALYEGKYPLGTALARPLIAKKLVEIARKEGADAVAHGCTGK 120 Query: 124 GNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFSIDT 183 GNDQVRFEL +L D+++IAPWR W K R++LI +AE+H IPI K+ P+SID Sbjct: 121 GNDQVRFELGIAALAPDLKVIAPWREWDLKSREELIAYAEEHGIPIPVTKKS--PYSIDA 178 Query: 184 NLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAINGQVMSPE 243 NL H S EG +LEDP PE VY+ VSPE+APD P + I+F++G P+AING+ +SP Sbjct: 179 NLWHRSIEGGILEDPWNEPPEDVYEWTVSPEDAPDEPEYVEIEFEKGVPVAINGEALSPA 238 Query: 244 VLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDSGSAH 303 L+E+LN+ +GIGRIDIVENR VGIKSRGVYETPGGTIL+ AHRA+ES++LD AH Sbjct: 239 ELIEELNELAGKHGIGRIDIVENRLVGIKSRGVYETPGGTILIKAHRALESLTLDREVAH 298 Query: 304 LKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRESNKS 363 KD+L +YA +VY G WFSP RE LQA ID++QE+V G + LKLYKGN +VVGR+S S Sbjct: 299 FKDELEPKYAELVYNGLWFSPLREALQAFIDETQEHVTGEVRLKLYKGNAIVVGRKSPNS 358 Query: 364 LYSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLARRNK 403 LY + L T+E+D D Y+Q D+EGFIKL L + A NK Sbjct: 359 LYDEDLATYEED-DVYDQKDAEGFIKLWGLPSKIAALVNK 397 >gnl|CDD|177791 PLN00200, PLN00200, argininosuccinate synthase; Provisional. Length = 404 Score = 612 bits (1581), Expect = e-176 Identities = 233/400 (58%), Positives = 301/400 (75%), Gaps = 3/400 (0%) Query: 1 MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQG-EELKIASDKARLLGAK 59 + + KVVLAYSGGLDTS+ILKWL+ G EV+ F AD+GQG EEL+ KA+ GAK Sbjct: 1 LRGKLNKVVLAYSGGLDTSVILKWLRENYGCEVVCFTADVGQGIEELEGLEAKAKASGAK 60 Query: 60 EVYVKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHG 119 ++ VKDLR EFVRD++FP RANA+YEG YLLGT++ARPLIAK +VDIA E GADA+AHG Sbjct: 61 QLVVKDLREEFVRDYIFPCLRANAIYEGKYLLGTSMARPLIAKAMVDIAKEVGADAVAHG 120 Query: 120 STGKGNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPF 179 +TGKGNDQVRFEL+ ++LN +++++APWR W KGR+DLI++A+KH IP+ K+ + + Sbjct: 121 ATGKGNDQVRFELTFFALNPELKVVAPWREWDIKGREDLIEYAKKHNIPVPVTKK--SIY 178 Query: 180 SIDTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAINGQV 239 S D NL H S EG +LEDP+ E ++ M VSPE APD P I I+F++G P+AING+ Sbjct: 179 SRDRNLWHISYEGDILEDPANEPKEDMFMMSVSPEAAPDQPEYIEIEFEKGLPVAINGKT 238 Query: 240 MSPEVLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDS 299 +SP LL +LN+ G +GIGRID+VENRFVG+KSRGVYETPGGTIL AHR +ES++LD Sbjct: 239 LSPATLLTKLNEIGGKHGIGRIDMVENRFVGMKSRGVYETPGGTILFAAHRELESLTLDR 298 Query: 300 GSAHLKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRE 359 + +KD L +YA +VY GFWF PERE + A ++K E GS+ LKLYKGNV V GR+ Sbjct: 299 ETMQVKDSLALKYAELVYNGFWFDPERESMDAFMEKITETTTGSVRLKLYKGNVSVAGRK 358 Query: 360 SNKSLYSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLA 399 S SLY + +FE+ YNQ+D+ GFI+L+ALRLRT A Sbjct: 359 SPYSLYRQDISSFEEGGGIYNQADAAGFIRLYALRLRTRA 398 >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 = 452 bits (1165), Expect = e-128 Identities = 191/399 (47%), Positives = 264/399 (66%), Gaps = 7/399 (1%) Query: 7 KVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEE-LKIASDKARLLGAKEVYVKD 65 KVVLAYSGGLDTS+ LKWL+ EKG EVI + AD+GQ EE + +KA GA+ Y D Sbjct: 1 KVVLAYSGGLDTSVCLKWLR-EKGYEVIAYTADVGQPEEDIDAIPEKALEYGAENHYTID 59 Query: 66 LRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGKGN 125 R EFV+D+ F +ANA YEG Y L TA+ARPLIAK LV+ A + GA+A+AHG TGKGN Sbjct: 60 AREEFVKDYGFAAIQANAFYEGTYPLSTALARPLIAKKLVEAAKKEGANAVAHGCTGKGN 119 Query: 126 DQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFSIDTNL 185 DQ RFE S LN D+++IAPWR +F R++ I++A + IP +K E P+SID NL Sbjct: 120 DQERFERSIRLLNPDLKVIAPWRDLNFT-REEEIEYAIQCGIPYPMSK--EKPYSIDENL 176 Query: 186 LHSSSEGRVLEDPSQPAPEYVYKMIVSPEEA-PDTPTTIRIDFQRGDPIAINGQVMSPEV 244 S E +LEDPS PE +Y P+EA PD P + IDF++G P+A+NG + P Sbjct: 177 WGRSIEAGILEDPSTEPPEDIYMWTKFPDEATPDEPEVVTIDFEQGVPVALNGVSLDPVE 236 Query: 245 LLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDSGSAHL 304 L+ + N+ +G+GRIDI+ENR +G+KSR +YE PG +L+ AHR +E+++L Sbjct: 237 LILEANEIAGKHGVGRIDIIENRIIGLKSREIYEAPGAALLIIAHRDLETLTLTRDVLEF 296 Query: 305 KDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRESNKSL 364 KD + +Y+ ++YQG WF P E L A I K+QE V G++ +KL+KGN +V+GR S SL Sbjct: 297 KDIVEEQYSELIYQGLWFDPLAEALDAFIRKTQERVTGTVRVKLFKGNAIVIGRTSPYSL 356 Query: 365 YSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLARRNK 403 Y ++LV+ E D D ++ D+ GFI + L+++ + K Sbjct: 357 YDEELVSMEKD-DVFDPRDAIGFITMRGLQIKDYREKKK 394 >gnl|CDD|184346 PRK13820, PRK13820, argininosuccinate synthase; Provisional. Length = 394 Score = 412 bits (1062), Expect = e-116 Identities = 191/403 (47%), Positives = 265/403 (65%), Gaps = 13/403 (3%) Query: 4 DVKKVVLAYSGGLDTSIILKWLQVEKGL-EVIVFIADLGQG-EELKIASDKARLLGAKEV 61 +KKVVLAYSGGLDTS+ + L+ + G EVI D+GQ EE+K A +KA+ LG K Sbjct: 1 MMKKVVLAYSGGLDTSVCVPLLKEKYGYDEVITVTVDVGQPEEEIKEAEEKAKKLGDKH- 59 Query: 62 YVKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGST 121 Y D + EF +D++FP +ANALYEGY LGTA+ARPLIA+ +V++A + GA AIAHG T Sbjct: 60 YTIDAKEEFAKDYIFPAIKANALYEGY-PLGTALARPLIAEKIVEVAEKEGASAIAHGCT 118 Query: 122 GKGNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFSI 181 GKGNDQ+RFE A SD+E+IAP R + R+ I++A++ IP+ K E P+SI Sbjct: 119 GKGNDQLRFE--AVFRASDLEVIAPIRELNLT-REWEIEYAKEKGIPVPVGK--EKPWSI 173 Query: 182 DTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAINGQVMS 241 D NL S EG LEDP+ PE +Y VSPE+APD P + I+F+ G P+AING+ M Sbjct: 174 DENLWSRSIEGGKLEDPAFEPPEEIYAWTVSPEDAPDEPEIVEIEFEEGVPVAINGEKMD 233 Query: 242 PEVLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISLDSGS 301 L+ +LN+ +G+GR D++E+R +G+KSR YE P T+LL AH+A+E + L Sbjct: 234 GVELIRKLNEIAGKHGVGRTDMMEDRVLGLKSRENYEHPAATVLLTAHKALEQLVLTREE 293 Query: 302 AHLKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVGRESN 361 K+ + S++A + Y+G P RE L A IDK+QE V G++T+KLYKG+ VVGRES Sbjct: 294 LKFKEIVDSKWAELAYEGLVDEPLREDLNAFIDKTQERVTGTVTVKLYKGSARVVGRESP 353 Query: 362 KSLYSDKLVTFED-DLDAYNQSDSEGFIKLHALRLRTLARRNK 403 +LYS++LV+F+ +D Q D+EG K H L+ R + + Sbjct: 354 YALYSEELVSFDSKTID---QRDAEGMAKYHGLQARLYNKVKR 393 >gnl|CDD|179859 PRK04527, PRK04527, argininosuccinate synthase; Provisional. Length = 400 Score = 201 bits (514), Expect = 2e-52 Identities = 127/406 (31%), Positives = 189/406 (46%), Gaps = 20/406 (4%) Query: 6 KKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLG--QGEELKIASDKARLLGAKEVYV 63 K +VLA+SGGLDTS + +LQ E+G V AD G EE +A LGA Sbjct: 3 KDIVLAFSGGLDTSFCIPYLQ-ERGYAVHTVFADTGGVDAEERDFIEKRAAELGAASHVT 61 Query: 64 KDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGK 123 D FV P+ A Y+G Y L + R LI + A E G IAHG TG Sbjct: 62 VDGGPAIWEGFVKPLVWAGEGYQGQYPLLVS-DRYLIVDAALKRAEELGTRIIAHGCTGM 120 Query: 124 GNDQVRFELSAYSLNSDIEIIAPWRHWSFKGRQDLIDFAEKH------AIPIDKNKRGEA 177 GNDQVRF+L+ +L D +I+AP R K + +K+ + + Sbjct: 121 GNDQVRFDLAVKAL-GDYQIVAPIREIQ-KEHTQTRAYEQKYLEERGFGVRAKQKA---- 174 Query: 178 PFSIDTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSPEEAPDTPTTIRIDFQRGDPIAING 237 ++I+ NLL + G ++ P E P T+ I F G+ +A++G Sbjct: 175 -YTINENLLGVTMSGGEIDRWEAPG-EGARGWCAPRSAWPTEALTVTIKFVEGEAVALDG 232 Query: 238 QVMSPEVLLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYETPGGTILLHAHRAIESISL 297 + + +L +LN+ G+GR + +G+K R V+E PG LL AHRA+E L Sbjct: 233 KPLPGAQILAKLNKLFAQYGVGRGVYTGDTVIGLKGRIVFEAPGLVSLLTAHRALEDAVL 292 Query: 298 DSGSAHLKDDLMSRYASIVYQGFWFSPEREMLQALIDKSQEYVEGSITLKLYKGNVMVVG 357 K D+ ++ +VY+GF+ P + ++A + SQ V G +TL+ G V V Sbjct: 293 TKQQNRFKPDVARKWVELVYEGFYHDPLKTDIEAFLKSSQAKVNGEVTLETRGGRVDAVA 352 Query: 358 RESNKSLYSDKLVTFEDDLDAYNQSDSEGFIKLHALRLRTLARRNK 403 S L + K T+ D + ++EGFIKL + A+ N+ Sbjct: 353 VRS-PHLLNSKGATYAQSAD-WGVEEAEGFIKLFGMSSTLYAQVNR 396 >gnl|CDD|180043 PRK05370, PRK05370, argininosuccinate synthase; Validated. Length = 447 Score = 128 bits (324), Expect = 3e-30 Identities = 113/385 (29%), Positives = 179/385 (46%), Gaps = 66/385 (17%) Query: 6 KKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIAS--DKARLLGAKEVYV 63 ++V +A+SGGLDTS L W++ +KG + A+LGQ +E + +A GA+ + Sbjct: 12 QRVGIAFSGGLDTSAALLWMR-QKGAVPYAYTANLGQPDEDDYDAIPRRAMEYGAENARL 70 Query: 64 KDLRREFVRDFVFPMFRANALYEGYYLLGTA---------IARPLIAKYLVDIANETGAD 114 D R + V + + A+ G + + T + R + LV E G + Sbjct: 71 IDCRAQLVAEGI------AAIQCGAFHISTGGVTYFNTTPLGRAVTGTMLVAAMKEDGVN 124 Query: 115 AIAHGSTGKGNDQVRFELSAYSL--NSDIEIIAPWRHWSF----KGRQDLIDFAEKHAIP 168 GST KGND RF Y L N +++I PW F GR ++ +F H Sbjct: 125 IWGDGSTYKGNDIERF--YRYGLLTNPELKIYKPWLDQDFIDELGGRAEMSEFLIAHGFD 182 Query: 169 IDKNKRGEAPFSIDTNLLHSSSEGRVLEDPSQPAPEYVYKMIVSP--------EEAPDTP 220 + E +S D+N+L ++ E + LE + IV+P E+ Sbjct: 183 YKMSV--EKAYSTDSNMLGATHEAKDLEHLNSGIK------IVNPIMGVAFWDEDVEIKA 234 Query: 221 TTIRIDFQRGDPIAINGQVMSPEV-LLEQLNQYGRCNGIGRIDIVENRFVGIKSRGVYET 279 + + F++G P+A+NG+ S V L+ + N+ G +G+G D +ENR + KSRG+YE Sbjct: 235 EEVTVRFEQGRPVALNGKTFSDPVELMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEA 294 Query: 280 PGGTILLHA--HRAIESISLDSGSAHLKDDLMS------RYASIVYQGFWFSPEREMLQA 331 P G LLH R + I H +D + R ++YQG WF P+ ML+ Sbjct: 295 P-GMALLHIAYERLVTGI-------HNEDTIEQYRINGRRLGRLLYQGRWFDPQALMLR- 345 Query: 332 LIDKSQEYV----EGSITLKLYKGN 352 + Q +V G +TL+L +GN Sbjct: 346 --ESLQRWVASAITGEVTLELRRGN 368 >gnl|CDD|178276 PLN02671, PLN02671, pectinesterase. Length = 359 Score = 35.6 bits (82), Expect = 0.025 Identities = 38/160 (23%), Positives = 61/160 (38%), Gaps = 23/160 (14%) Query: 42 QGEELKIASDKA-----RLLGAKEVYVKDLRREFVR--------DFVFPMFRANALYEGY 88 Q L+I+ DKA R+LGA++ + + + DF+F A +LY+ Sbjct: 177 QAVALRISGDKAFFYKVRVLGAQDTLLDETGSHYFYQCYIQGSVDFIFG--NAKSLYQDC 234 Query: 89 YLLGTAIARPLIAKYLVDIANE------TGADAIAHGSTGKGNDQVRFELSAYSLNSDIE 142 + TA IA + D E G G + + YS + Sbjct: 235 VIQSTAKRSGAIAAHHRDSPTEDTGFSFVNCVINGTGKIYLGRAWGNYSRTVYSNCFIAD 294 Query: 143 IIAP--WRHWSFKGRQDLIDFAEKHAIPIDKNKRGEAPFS 180 II P W W++ RQ + F E + ++ G P+S Sbjct: 295 IITPSGWSDWNYPERQRTVMFGEYNCSGRGADRGGRVPWS 334 >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 = 34.8 bits (80), Expect = 0.037 Identities = 38/145 (26%), Positives = 64/145 (44%), Gaps = 21/145 (14%) Query: 6 KKVVLAYSGGLDTSIILKWLQVEKGLEV--IVFIADLGQGEELKIASDKARLLGAKEVYV 63 KKV++AYSGG+D+S++ + G EV I ++ EL+ A A+ +G Sbjct: 13 KKVLIAYSGGVDSSLLAAVCS-DAGTEVLAITVVSPSISPRELEDAIIIAKEIG------ 65 Query: 64 KDLRREFVR-DFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTG 122 + EFV+ D + FRAN Y+ + ++ LV A + G D + G+ Sbjct: 66 --VNHEFVKIDKMINPFRANVEERCYF------CKKMVLSILVKEAEKRGYDVVVDGTNA 117 Query: 123 KGNDQVRFELSAYSLNSDIEIIAPW 147 D + Y + ++PW Sbjct: 118 ---DDLFDHRPGYRAVKEFNGVSPW 139 >gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA; Provisional. Length = 362 Score = 33.0 bits (75), Expect = 0.14 Identities = 35/130 (26%), Positives = 60/130 (46%), Gaps = 26/130 (20%) Query: 1 MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDK---ARLLG 57 M K+V++ SGG+D++ LQ E+G E++ G +++ D+ AR L Sbjct: 1 MKESKKRVLVGMSGGIDSTATCLMLQ-EQGYEIV--------GVTMRVWGDEPQDARELA 51 Query: 58 AK---EVYVKDLRREF----VRDFVFPMFRANALYEGYYLLGTAIARPLIA-KYLVDIAN 109 A+ E YV D R F V++F+ + +G + PL + L++ A+ Sbjct: 52 ARMGIEHYVADERVPFKDTIVKNFI------DEYRQGRTPNPCVMCNPLFKFRMLIEWAD 105 Query: 110 ETGADAIAHG 119 + G IA G Sbjct: 106 KLGCAWIATG 115 >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 = 32.6 bits (75), Expect = 0.19 Identities = 36/182 (19%), Positives = 67/182 (36%), Gaps = 34/182 (18%) Query: 7 KVVLAYSGGLDTSI---ILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKEVYV 63 ++++A SGG+D+ +L LQ + + +I D G E SD+ +V Sbjct: 1 RILVAVSGGVDSMALLHLLLKLQPKLKIRLIAAHVDHGLRPE----SDEE------AEFV 50 Query: 64 KDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGADAIAHGSTGK 123 + ++ AL +G AR + +IA + GAD I Sbjct: 51 QQFCKKLNIPLEIKKVDVKALAKGKKKNLEEAAREARYDFFEEIAKKHGADYILTAHH-- 108 Query: 124 GNDQV------------RFELSAY----SLNSDIEIIAPWRHWSFKGRQDLIDFAEKHAI 167 +DQ LS L + +II P S + ++ ++ +++ + Sbjct: 109 ADDQAETILLRLLRGSGLRGLSGMKPIRILGNGGQIIRPLLGIS---KSEIEEYLKENGL 165 Query: 168 PI 169 P Sbjct: 166 PW 167 >gnl|CDD|165411 PHA03139, PHA03139, helicase-primase primase subunit; Provisional. Length = 860 Score = 32.3 bits (73), Expect = 0.24 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 8/53 (15%) Query: 46 LKI-ASDKARLLGAKEVYVKDLRREFVRDFV---FPMFRANALYEGYYLLGTA 94 L+I ASDK + K +Y RR+ + FP+FR L++ + G + Sbjct: 378 LEISASDKYVQIQDKRIY----RRQHLHKDYHRPFPVFRVQLLHKNIFCFGNS 426 >gnl|CDD|178898 PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed. Length = 346 Score = 30.8 bits (71), Expect = 0.58 Identities = 41/138 (29%), Positives = 55/138 (39%), Gaps = 36/138 (26%) Query: 6 KKVVLAYSGGLDTSIILKWLQVEKGLEVI-VFIADLGQGEELKI--------ASDKARLL 56 K+VV+ SGG+D+S+ L E+G EVI VF+ L ++ AR + Sbjct: 1 KRVVVGMSGGVDSSVAA-ALLKEQGYEVIGVFMK-LWDDDDETGKGGCCAEEDIADARRV 58 Query: 57 GAK---EVYVKDLRREFVRDFVF-PMFRANALYEGYYLLG-TAIARPLIA-------KYL 104 K YV D +EF D V Y G T P + K Sbjct: 59 ADKLGIPHYVVDFEKEF-WDRVIDYFLDE-------YKAGRTPN--PCVLCNKEIKFKAF 108 Query: 105 VDIANETGADAIAHGSTG 122 ++ A E GAD IA TG Sbjct: 109 LEYARELGADYIA---TG 123 >gnl|CDD|148238 pfam06508, ExsB, ExsB. This family includes putative transcriptional regulators from Bacteria and Archaea. Length = 137 Score = 29.9 bits (68), Expect = 1.4 Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 3/55 (5%) Query: 7 KVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGE--ELKIASDKARLLGAK 59 K V+ SGGLD++ L W + ++G EV D GQ EL+ A A+ LG + Sbjct: 1 KAVVLLSGGLDSTTCLAWAK-KEGYEVYALTFDYGQRHSKELECAKKIAKALGVE 54 >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 = 29.7 bits (67), Expect = 1.5 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 3/54 (5%) Query: 9 VLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQ--GEELKIASDKARLLGAKE 60 V+ SGG D++ L + E G EV D GQ EL+ A A LG + Sbjct: 2 VVVLSGGQDSTTCLAIAKDE-GYEVHAITFDYGQRHSRELESARKIAEALGIEH 54 >gnl|CDD|131719 TIGR02671, cas_csx9, CRISPR-associated protein (provisional), Csx9 family. Members of this family, so far, are archaeal proteins found in CRISPR-associated (cas) gene regions. So far, this rare cas protein is found in only three genomes: Pyrococcus horikoshii shinkaj OT3, Pyrococcus abyssi GE5, and Thermococcus kodakarensis KOD1. In each case it is found immediately upstream of cas3 in loci that resemble the Apern type but lack Csa1 and Csa4 genes. Length = 377 Score = 29.5 bits (66), Expect = 1.6 Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 10/95 (10%) Query: 1 MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKE 60 ++ VKK+ GG+D + LK + + D+ + E K S +L Sbjct: 260 LAEYVKKIENYRVGGVDLLVELKEGGATVEKYPLWALVDIAEKELWKGVSGDREMLAY-- 317 Query: 61 VYVKDL-------RREFVRDFVFPMFR-ANALYEG 87 ++VKDL R+E + D +F +FR AL EG Sbjct: 318 IFVKDLYRAINSGRKELIEDSIFRLFRQGRALLEG 352 >gnl|CDD|118190 pfam09658, Cas_Csx9, CRISPR-associated protein (Cas_Csx9). Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes archaeal proteins encoded in cas gene regions. Length = 377 Score = 29.5 bits (66), Expect = 1.6 Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 10/95 (10%) Query: 1 MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEVIVFIADLGQGEELKIASDKARLLGAKE 60 ++ VKK+ GG+D + LK + + D+ + E K S +L Sbjct: 260 LAEYVKKIENYRVGGVDLLVELKEGGATVEKYPLWALVDIAEKELWKGVSGDREMLAY-- 317 Query: 61 VYVKDL-------RREFVRDFVFPMFR-ANALYEG 87 ++VKDL R+E + D +F +FR AL EG Sbjct: 318 IFVKDLYRAINSGRKELIEDSIFRLFRQGRALLEG 352 >gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional. Length = 436 Score = 29.2 bits (66), Expect = 2.1 Identities = 7/17 (41%), Positives = 17/17 (100%) Query: 6 KKVVLAYSGGLDTSIIL 22 +++++A+SGGLD++++L Sbjct: 16 RQILVAFSGGLDSTVLL 32 >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 = 28.9 bits (65), Expect = 2.3 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 14/88 (15%) Query: 6 KKVVLAYSGGLDTSIILKWLQVEKGLEVI-VFIA-----DLGQG------EELKIASDKA 53 KKV++ SGG+D+S+ +L ++G EV+ VF+ D G E+L+ A Sbjct: 1 KKVIVGLSGGVDSSVSA-YLLKQQGYEVVGVFMKNWEEDDKNDGHGCTSAEDLRDAQAIC 59 Query: 54 RLLGAKEVYVKDLRREFVRDFVFPMFRA 81 LG + + ++E+ P + Sbjct: 60 EKLGIP-LEKVNFQKEYWNKVFEPFIQE 86 >gnl|CDD|118641 pfam10113, Fibrillarin_2, Fibrillarin-like archaeal protein. Members of this family of proteins include archaeal fibrillarin homologs. Length = 505 Score = 28.2 bits (63), Expect = 3.8 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 10/76 (13%) Query: 42 QGEELKIASDKARLLGAKEVYVKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIA 101 Q EEL+ + R LG+ VY +D+ ++ D + ++ YE R + Sbjct: 352 QKEELEALARAVRFLGSNLVYPRDIGGTYIGDAHWAALPSSPAYE----------RSDVV 401 Query: 102 KYLVDIANETGADAIA 117 K + D+ +E AD +A Sbjct: 402 KTVDDLESEVIADTVA 417 >gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated. Length = 251 Score = 28.1 bits (63), Expect = 4.1 Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 4/32 (12%) Query: 91 LGTAIARPLI---AK-YLVDIANETGADAIAH 118 LG AIAR + AK +L DI + G DA A Sbjct: 11 LGRAIARRMAEQGAKVFLTDINDAAGLDAFAA 42 >gnl|CDD|163331 TIGR03569, NeuB_NnaB, N-acetylneuraminate synthase. This family is a subset of the Pfam model pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine. Length = 329 Score = 27.9 bits (63), Expect = 4.4 Identities = 11/19 (57%), Positives = 13/19 (68%) Query: 100 IAKYLVDIANETGADAIAH 118 +AK LVD A E GADA+ Sbjct: 17 LAKKLVDAAAEAGADAVKF 35 >gnl|CDD|182880 PRK10982, PRK10982, galactose/methyl galaxtoside transporter ATP-binding protein; Provisional. Length = 491 Score = 27.8 bits (62), Expect = 5.0 Identities = 18/45 (40%), Positives = 21/45 (46%), Gaps = 11/45 (24%) Query: 257 GIGRIDIVENRFVGIKSRGVYETPGGTILLHA-----HRAIESIS 296 G R DIVE F G+ E GTI LH H A E+I+ Sbjct: 284 GAKRTDIVETLF------GIREKSAGTITLHGKKINNHNANEAIN 322 >gnl|CDD|148126 pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences. Length = 294 Score = 28.0 bits (63), Expect = 5.1 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 10/52 (19%) Query: 18 TSIILKWL--QVEKGLEVIVFIADLGQGEE-LKIASDKARLLGAKEVYVKDL 66 T++ L+ L V+ G V+ D+G G L IA A LGAK+V D+ Sbjct: 147 TALCLEALESLVKPGETVL----DVGCGSGILAIA---ALKLGAKKVVGVDI 191 >gnl|CDD|173128 PRK14665, mnmA, tRNA-specific 2-thiouridylase MnmA; Provisional. Length = 360 Score = 28.0 bits (62), Expect = 5.1 Identities = 35/125 (28%), Positives = 52/125 (41%), Gaps = 11/125 (8%) Query: 1 MSRDVKKVVLAYSGGLDTSIILKWLQVEKGLEV----IVFIADLGQGEELKIASDKARLL 56 M K+V+L SGG D+S+ L E G EV F G E L+ A A L Sbjct: 1 MMEKNKRVLLGMSGGTDSSVAAMLLL-EAGYEVTGVTFRFYEFNGSTEYLEDARALAERL 59 Query: 57 GAKEVY--VKDLRREFVRDFVFPMFRANALYEGYYLLGTAIARPLIAKYLVDIANETGAD 114 G + + + R+ + D+ + + L + PL+AK IA+E G Sbjct: 60 GIGHITYDARKVFRKQIIDYFIDEYMSGHTPVPCTLCNNYLKWPLLAK----IADEMGIF 115 Query: 115 AIAHG 119 +A G Sbjct: 116 YLATG 120 >gnl|CDD|150740 pfam10100, DUF2338, Uncharacterized protein conserved in bacteria (DUF2338). Members of this family of hypothetical bacterial proteins have no known function. Length = 429 Score = 27.4 bits (61), Expect = 6.4 Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 3/26 (11%) Query: 199 SQPAPEYVYKMIVSPEEAPDTPTTIR 224 P+YVYK+ E P TPT IR Sbjct: 231 ETKVPKYVYKLY---PEGPITPTLIR 253 >gnl|CDD|179053 PRK00517, prmA, ribosomal protein L11 methyltransferase; Reviewed. Length = 250 Score = 27.4 bits (62), Expect = 7.4 Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 10/48 (20%) Query: 18 TSIILKWL--QVEKGLEVIVFIADLGQGEE-LKIASDKARLLGAKEVY 62 T + L+ L V G V+ D+G G L IA A LGAK+V Sbjct: 106 TRLCLEALEKLVLPGKTVL----DVGCGSGILAIA---AAKLGAKKVL 146 >gnl|CDD|181524 PRK08654, PRK08654, pyruvate carboxylase subunit A; Validated. Length = 499 Score = 27.3 bits (61), Expect = 8.4 Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 12/44 (27%) Query: 82 NALYEGY----YLLGTAIARPLIAKYL-----VDIANETGADAI 116 NAL+ Y Y +G A P YL +D+A + GADAI Sbjct: 38 NALFVKYADEAYPIGPA---PPSKSYLNIERIIDVAKKAGADAI 78 >gnl|CDD|182110 PRK09849, PRK09849, putative oxidoreductase; Provisional. Length = 702 Score = 26.9 bits (60), Expect = 9.0 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%) Query: 154 GRQDLIDFAEKHAIPIDKNKRGEAPFSIDTNLLHSS 189 G +D D K+ PI+ K A +S+ N LH S Sbjct: 522 GSEDAYD-ETKNYTPINDAKAKFAKWSLLRNCLHDS 556 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 0.318 0.137 0.393 Gapped Lambda K H 0.267 0.0790 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 6,795,843 Number of extensions: 456501 Number of successful extensions: 918 Number of sequences better than 10.0: 1 Number of HSP's gapped: 890 Number of HSP's successfully gapped: 40 Length of query: 404 Length of database: 5,994,473 Length adjustment: 96 Effective length of query: 308 Effective length of database: 3,920,105 Effective search space: 1207392340 Effective search space used: 1207392340 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: 58 (26.0 bits)