RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781179|ref|YP_003065592.1| D-alanine--D-alanine ligase [Candidatus Liberibacter asiaticus str. psy62] (300 letters) >gnl|CDD|179288 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed. Length = 304 Score = 407 bits (1049), Expect = e-114 Identities = 134/301 (44%), Positives = 187/301 (62%), Gaps = 6/301 (1%) Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFNVLHGN 61 AVLMGG S+EREVSL+SG A +AL +AG+ ID + L L D FN LHG Sbjct: 8 AVLMGGTSAEREVSLNSGAAVLAALREAGYDAHPIDPGEDIAAQLKELGFDRVFNALHGR 67 Query: 62 FGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQ 121 GEDG +Q +LELL IPYT SG+LASAL+MDK+R+K V + G+P P I++ R Sbjct: 68 GGEDGTIQGLLELLGIPYTGSGVLASALAMDKLRTKLVWQAAGLPTPPWIVLTREEDLLA 127 Query: 122 --HLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTC 179 + P V+KP + GSS+G+ +K++ + L ++ + D++L+E+Y+ G ELT Sbjct: 128 AIDKLGLPLVVKPAREGSSVGVSKVKEEDELQAAL--ELAFKYDDEVLVEKYIKGRELTV 185 Query: 180 GVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIG 239 V+G +L V EI VP +FY YE KY + + ++ PA +P +I E+Q LA A++A+G Sbjct: 186 AVLGGKALPVIEI-VPAGEFYDYEAKYLAGGTQYICPAGLPAEIEAELQELALKAYRALG 244 Query: 240 CRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDASCL 299 CRG R DF+ D K + LE+N QPGMT S+ P A AG SF EL+ ++EDA C Sbjct: 245 CRGWGRVDFMLDE-DGKPYLLEVNTQPGMTSHSLVPMAARAAGISFSELVDRILEDALCD 303 Query: 300 R 300 R Sbjct: 304 R 304 >gnl|CDD|162248 TIGR01205, D_ala_D_alaTIGR, D-alanine--D-alanine ligase. but a number of antibiotic resistance proteins score above the trusted cutoff of this model. Length = 315 Score = 266 bits (683), Expect = 4e-72 Identities = 113/318 (35%), Positives = 184/318 (57%), Gaps = 28/318 (8%) Query: 2 AVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAHL------------ 49 AVL GG S+E E+SL S A AL D G+ V +D+D+ L Sbjct: 3 AVLFGGKSAEHEISLVSAAAVLKALRDLGYDVYPVDIDKMGSWTYKDLPQLILELGALLE 62 Query: 50 KPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCP 109 D+ F VLHG +GEDG +Q +LEL+ IPYT SG+LASALSMDK+ +K + + G+P Sbjct: 63 GIDVVFPVLHGRYGEDGTIQGLLELMGIPYTGSGVLASALSMDKLLTKLLWKALGLPTPD 122 Query: 110 SILVNRF-----TMDSQHLISP---PYVIKPLKGGSSLGIIVIK-KDQSIP-LDLLQSSS 159 I++ + ++ + + P P ++KP + GSS+G+ +K +++ LD Sbjct: 123 YIVLTQNRASADELECEQVAEPLGFPVIVKPAREGSSVGVSKVKSEEELQAALDEAFE-- 180 Query: 160 WNHGDQLLIEQYVDGIELTCGVMG-DASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAK 218 + +++L+EQ++ G EL ++G + +L + EI FY YE KY ++ +V+PA Sbjct: 181 --YDEEVLVEQFIKGRELEVSILGNEEALPIIEIVPEIEGFYDYEAKYLDGSTEYVIPAP 238 Query: 219 IPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMA 278 + ++ ++++ LA A++A+GCRG++R DF D +++ EIN PGMT +S+FP+ A Sbjct: 239 LDEELEEKIKELALKAYKALGCRGLARVDFFLDE-EGEIYLNEINTIPGMTAISLFPKAA 297 Query: 279 AYAGYSFRELLLWMVEDA 296 A AG F +L+ ++E A Sbjct: 298 AAAGIEFSQLVERILELA 315 >gnl|CDD|179356 PRK01966, ddl, D-alanyl-alanine synthetase A; Reviewed. Length = 333 Score = 240 bits (615), Expect = 4e-64 Identities = 111/332 (33%), Positives = 180/332 (54%), Gaps = 44/332 (13%) Query: 2 AVLMGGISSEREVSLSSGKACASAL---------------------EDAGFKVSQIDVDR 40 A+L GG S+E EVSL S K+ AL + +++ D D+ Sbjct: 7 ALLFGGRSAEHEVSLVSAKSVLKALDKEKYEVVPIGITKDGRWYLIDADNMELADDDNDK 66 Query: 41 SVGLVLAHLKP-----DLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMR 95 +L D+ F VLHG GEDG +Q +LELL IPY G+LASALSMDK+ Sbjct: 67 EDLSLLILPSGGSEEVDVVFPVLHGPPGEDGTIQGLLELLGIPYVGCGVLASALSMDKIL 126 Query: 96 SKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLKGGSSLGI-IVIKKDQ 148 +K+++++ G+PV P +++ R + L + P +KP GSS+GI V +++ Sbjct: 127 TKRLLAAAGIPVAPYVVLTRGDWEEASLAEIEAKLGLPVFVKPANLGSSVGISKVKNEEE 186 Query: 149 SIP-LDLLQSSSWNHGDQLLIEQYVDGIELTCGVMG---DASLDVTEIAVPKSDFYSYEL 204 LDL ++ + ++L+EQ + G E+ C V+G AS+ EI V DFY YE Sbjct: 187 LAAALDL----AFEYDRKVLVEQGIKGREIECAVLGNDPKASV-PGEI-VKPDDFYDYEA 240 Query: 205 KYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINV 264 KY ++ ++PA + ++ ++++ LA A +A+GC G++R DF +++ EIN Sbjct: 241 KYLDGSAELIIPADLSEELTEKIRELAIKAFKALGCSGLARVDFFLTE-DGEIYLNEINT 299 Query: 265 QPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296 PG TP+S++P++ +G S+ EL+ ++E A Sbjct: 300 MPGFTPISMYPKLWEASGLSYPELIDRLIELA 331 >gnl|CDD|184751 PRK14571, PRK14571, D-alanyl-alanine synthetase A; Provisional. Length = 299 Score = 188 bits (478), Expect = 2e-48 Identities = 100/305 (32%), Positives = 159/305 (52%), Gaps = 21/305 (6%) Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAHLKP-DLAFNVLH 59 +A+LMGG+S ERE+SL SG+ ALE G++V+ DVD + LK D+ FNVLH Sbjct: 3 VALLMGGVSREREISLRSGERVKKALEKLGYEVTVFDVDEDFLKKVDQLKSFDVVFNVLH 62 Query: 60 GNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMD 119 G FGEDG +QAIL+ L I YT S +S + DK+ + + + ++ + F Sbjct: 63 GTFGEDGTLQAILDFLGIRYTGSDAFSSMICFDKLLTYRFLKG-------TVEIPDFVEI 115 Query: 120 SQHLISPPY----VIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGI 175 + + + P V+KP + GSS+G+ + + D+ L +++++Y+ G Sbjct: 116 KEFMKTSPLGYPCVVKPRREGSSIGVFICESDEEFQHAL--KEDLPRYGSVIVQEYIPGR 173 Query: 176 ELTCGVM----GDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLA 231 E+T ++ G L + E+ PK FY Y KY+ + +LPA + + + V+ A Sbjct: 174 EMTVSILETEKGFEVLPILELR-PKRRFYDYVAKYTKGETEFILPAPLNPEEERLVKETA 232 Query: 232 FLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLW 291 A GCRG R D +F + ++LEIN PG+T +S P A G F EL+ Sbjct: 233 LKAFVEAGCRGFGRVDGIFS--DGRFYFLEINTVPGLTELSDLPASAKAGGIEFEELVDI 290 Query: 292 MVEDA 296 +++ A Sbjct: 291 IIKSA 295 >gnl|CDD|173036 PRK14572, PRK14572, D-alanyl-alanine synthetase A; Provisional. Length = 347 Score = 168 bits (428), Expect = 1e-42 Identities = 105/347 (30%), Positives = 162/347 (46%), Gaps = 60/347 (17%) Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLV--------------- 45 +AV GG S+E +S+ +G + L G V I + G V Sbjct: 4 IAVFFGGSSTEHSISIRTGCFICATLHTMGHSVKPILLTPDGGWVVPTVYRPSIPDESGN 63 Query: 46 --------------------LAHLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGIL 85 ++ L D+AF LHG GEDG +Q L+ L IPYT SG+L Sbjct: 64 SEDLFLEEFQKANGVSEPADISQLDADIAFLGLHGGAGEDGRIQGFLDTLGIPYTGSGVL 123 Query: 86 ASALSMDKMRSKQVVSSCGVPVCPSILVNR--FTMDSQHLI------SPPYVIKPLKGGS 137 ASAL+MDK R+ Q+ G V P + + + + + P +KP++GGS Sbjct: 124 ASALAMDKTRANQIFLQSGQKVAPFFELEKLKYLNSPRKTLLKLESLGFPQFLKPVEGGS 183 Query: 138 SLGIIVIKKDQSIP--LDLLQSSSWNHGDQLLIEQYVDGIELTCGVM--------GDASL 187 S+ I + + L L+ S +++ + ++ G E++CGV+ +L Sbjct: 184 SVSTYKITNAEQLMTLLALIFESD----SKVMSQSFLSGTEVSCGVLERYRGGKRNPIAL 239 Query: 188 DVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSD 247 TEI VP +F+ +E KY S + PA+I K VQ LA AH+++GC+G SR+D Sbjct: 240 PATEI-VPGGEFFDFESKYKQGGSEEITPARISDQEMKRVQELAIRAHESLGCKGYSRTD 298 Query: 248 FLFDPLSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVE 294 F+ + + LE N PGMT S+ P+ A AG + E+ ++E Sbjct: 299 FII--VDGEPHILETNTLPGMTETSLIPQQAKAAGINMEEVFTDLIE 343 >gnl|CDD|173033 PRK14569, PRK14569, D-alanyl-alanine synthetase A; Provisional. Length = 296 Score = 157 bits (399), Expect = 2e-39 Identities = 109/299 (36%), Positives = 165/299 (55%), Gaps = 12/299 (4%) Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVD-RSVGLVLAHLKPDLAFNVLH 59 + VL GG S EREVSL SGKA +L G+ +D + + L LKPD F LH Sbjct: 6 IVVLYGGDSPEREVSLKSGKAVLDSLISQGYDAVGVDASGKELVAKLLELKPDKCFVALH 65 Query: 60 GNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPV-CPSILVNRFTM 118 G GE+G V A+LE+LEI +T S + +S ++MDKM SK+++ +P L ++ Sbjct: 66 GEDGENGRVSALLEMLEIKHTSSSMKSSVITMDKMISKEILMHHRMPTPMAKFLTDKLVA 125 Query: 119 DSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELT 178 + + IS P +KP GGSS+ +K Q + ++S +G +++IEQ+V G E+T Sbjct: 126 EDE--ISFPVAVKPSSGGSSIATFKVKSIQELKHAYEEAS--KYG-EVMIEQWVTGKEIT 180 Query: 179 CGVMGDASLDVTEIAVPKSDFYSYELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAI 238 ++ D I P+++FY YE KYS + H P+ + EV++LA A+ + Sbjct: 181 VAIVNDEVYSSVWIE-PQNEFYDYESKYSGKSIYHS-PSGLCEQKELEVRQLAKKAYDLL 238 Query: 239 GCRGISRSDFLFDPLSRKVFW-LEINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296 GC G +R DF++D R F+ +EIN PGMT S+ P+ AA G F + ++E A Sbjct: 239 GCSGHARVDFIYD--DRGNFYIMEINSSPGMTDNSLSPKSAAAEGVDFDSFVKRIIEQA 295 >gnl|CDD|148851 pfam07478, Dala_Dala_lig_C, D-ala D-ala ligase C-terminus. This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). Length = 201 Score = 138 bits (350), Expect = 2e-33 Identities = 64/207 (30%), Positives = 121/207 (58%), Gaps = 17/207 (8%) Query: 99 VVSSCGVPVCPSILVNR--FTMDS-QHLISP---PYVIKPLKGGSSLGIIVIKKDQSIPL 152 ++ + G+PV P I++ R + + + + + P +KP GSS+GI K S Sbjct: 1 LLKAAGIPVAPFIVLTREDWVLATIEKVEEKLGYPVFVKPANLGSSVGI---SKVTS--R 55 Query: 153 DLLQSS---SWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEIA--VPKSDFYSYELKYS 207 + LQS+ ++ + +++LIE+ ++G E+ C V+G+ L+V+ + FY YE KY Sbjct: 56 EELQSAIEEAFQYDNKVLIEEAIEGREIECAVLGNEDLEVSPVGEIRLSGGFYDYEAKYI 115 Query: 208 SLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEINVQPG 267 ++ ++PA +P ++ +++Q LA A++A+GCRG++R DF +++ E+N PG Sbjct: 116 LSSAQIIVPADLPEEVEEQIQELALKAYKALGCRGLARIDFFLTE-DGEIYLNEVNTMPG 174 Query: 268 MTPVSIFPEMAAYAGYSFRELLLWMVE 294 T +S++P M A AG S+ +L+ ++E Sbjct: 175 FTSISLYPRMWAAAGLSYPDLIDQLIE 201 >gnl|CDD|184750 PRK14568, vanB, D-alanine--D-lactate ligase; Provisional. Length = 343 Score = 133 bits (337), Expect = 5e-32 Identities = 105/333 (31%), Positives = 151/333 (45%), Gaps = 49/333 (14%) Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDV---------------------- 38 + +L GG S E VS+ S A L+ ++ I + Sbjct: 6 VGILFGGCSEEHPVSVKSAIEVARNLDTEKYEPFYIGITKSGVWKLCDGPCAEWENGSCR 65 Query: 39 ------DRSVG--LVLAH-----LKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGIL 85 DR V LVL ++ D+ F VLHG GEDG +Q +LEL IPY I Sbjct: 66 PAVLSPDRKVHGLLVLEQGEYETIRLDVVFPVLHGKLGEDGAIQGLLELSGIPYVGCDIQ 125 Query: 86 ASALSMDKMRSKQVVSSCGVPVCPS--ILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIV 143 +SAL MDK + V + G+ P+ + D+ L P +V KP + GSS G V Sbjct: 126 SSALCMDKSLAYIVAKNAGIAT-PAFWTVTADERPDAATLTYPVFV-KPARSGSSFG--V 181 Query: 144 IKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMG-DASL---DVTEIAVPKSDF 199 K + + LD S+ + ++LIE+ V G E+ C V+G A L +V +I + F Sbjct: 182 SKVNSADELDYAIESARQYDSKVLIEEAVVGSEVGCAVLGNGADLVVGEVDQIRLSHGFF 241 Query: 200 YSY---ELKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRK 256 + E + S NST ++PA I + VQ A ++A+GCRG++R D Sbjct: 242 RIHQENEPEKGSENSTIIVPADISAEERSRVQETAKAIYRALGCRGLARVDMFLQEDGTV 301 Query: 257 VFWLEINVQPGMTPVSIFPEMAAYAGYSFRELL 289 V E+N PG T S +P M A AG EL+ Sbjct: 302 VL-NEVNTLPGFTSYSRYPRMMAAAGIPLAELI 333 >gnl|CDD|173034 PRK14570, PRK14570, D-alanyl-alanine synthetase A; Provisional. Length = 364 Score = 128 bits (324), Expect = 1e-30 Identities = 88/337 (26%), Positives = 166/337 (49%), Gaps = 50/337 (14%) Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAG-FKVSQIDVDRSVGL--------------- 44 + ++ GG+S E E+SL S SAL + + + +D+ G+ Sbjct: 5 LMLIFGGVSFEHEISLRSAYGIYSALLKLDKYNIYSVFIDKCTGIWYLLDSVPDPPKLIK 64 Query: 45 --VLA---------------HLKPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILAS 87 VL +L+ D+ F ++HG GEDG +Q L++++IP +GIL S Sbjct: 65 RDVLPIVSLIPGCGIFVNNKNLEIDVVFPIVHGRTGEDGAIQGFLKVMDIPCVGAGILGS 124 Query: 88 ALSMDKMRSKQVVSSCGVPVCPSILVNRFTM---------DSQHLISPPYVIKPLKGGSS 138 A+S++K K ++ S +P+ P I ++ D + ++ P ++KP GSS Sbjct: 125 AISINKYFCKLLLKSFNIPLVPFIGFRKYDYFLDKEGIKKDIKEVLGYPVIVKPAVLGSS 184 Query: 139 LGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDV---TEIAVP 195 +GI V + I + ++ + ++IE++++ E+ C V+G+ + + EI V Sbjct: 185 IGINVAYNENQI--EKCIEEAFKYDLTVVIEKFIEAREIECSVIGNEQIKIFTPGEIVVQ 242 Query: 196 KSDFYSYELKYSSLNSTHV---LPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDP 252 FY Y+ KYS++ + +PA + +++ AFL ++ + RG++R DFL + Sbjct: 243 DFIFYDYDAKYSTIPGNSIVFNIPAHLDTKHLLDIKEYAFLTYKNLELRGMARIDFLIEK 302 Query: 253 LSRKVFWLEINVQPGMTPVSIFPEMAAYAGYSFRELL 289 + ++ EIN PG T +S+F +M + G ++ L+ Sbjct: 303 DTGLIYLNEINTIPGFTDISMFAKMCEHDGLQYKSLV 339 >gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase A/UDP-N-acetylmuramate--L-alanine ligase; Provisional. Length = 809 Score = 100 bits (250), Expect = 5e-22 Identities = 92/341 (26%), Positives = 146/341 (42%), Gaps = 53/341 (15%) Query: 1 MAVLMGGISSEREVSLSSGKACASALEDAGFKVSQIDVDR----SVGLVLAHL------- 49 + ++ GG S E ++SL S K A L + VS ++R L Sbjct: 454 LGLVCGGKSCEHDISLLSAKNIAKYLSPEFYDVSYFLINRQGLWETVSSLETAIEEDSGK 513 Query: 50 ------------KPDLAFNVLHGNFGEDGLVQAILELLEIPYTHSGILASALSMDKMRSK 97 K D+ +LHG FGEDG +Q LE++ PYT + SA++MDK+ +K Sbjct: 514 SVLSSEIAQALAKVDVVLPILHGPFGEDGTMQGFLEIIGKPYTGPSLAFSAIAMDKVLTK 573 Query: 98 QVVSSCGVPVCPSILVNRFTMDS------QHLI---SPPYVIKPLKGGSSLGIIVIKKDQ 148 + S GVPV P + H++ S P +K GSS+G+ + + Sbjct: 574 RFASDVGVPVVPYQPLTLAGWKREPELCLAHIVEAFSFPMFVKTAHLGSSIGVFEVHNVE 633 Query: 149 SIPLDLLQSSSWNHGDQLLIEQYVDG---IELTCGVMGDASLDVTEIAVP-----KSDFY 200 + + S ++ + + +E+ G IE++C +GD S IA P F Sbjct: 634 ELRDKI--SEAFLYDTDVFVEESRLGSREIEVSC--LGDGS-SAYVIAGPHERRGSGGFI 688 Query: 201 SYELKYSSLNSTHVLPAKIPLDIYKE----VQRLAFLAHQAIGCRGISRSDFLFDPLSRK 256 Y+ KY L+ LD+ KE V LA ++ + +G R DF D Sbjct: 689 DYQEKY-GLSGKSSAQIVFDLDLSKESQEQVLELAERIYRLLQGKGSCRIDFFLD--EEG 745 Query: 257 VFWL-EINVQPGMTPVSIFPEMAAYAGYSFRELLLWMVEDA 296 FWL E+N PGMT S F G+++ +++ ++ D Sbjct: 746 NFWLSEMNPIPGMTEASPFLTAFVRKGWTYEQIVHQLIIDG 786 >gnl|CDD|183732 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein; Provisional. Length = 326 Score = 45.6 bits (109), Expect = 1e-05 Identities = 44/214 (20%), Positives = 87/214 (40%), Gaps = 36/214 (16%) Query: 89 LSMDKMRSKQVVSSCGVPVCPSILVN----RFTMDSQHLISPPYVIKPLKGGSSLGI-IV 143 + DK + + + G+P S L ++ + P +KP G +S+G+ V Sbjct: 108 ICNDKWLTYEFLKENGIPTPKSYLPESLEDFKAALAKGELQFPLFVKPRDGSASIGVFKV 167 Query: 144 IKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDASLDVTEIAVPKSDFYSYE 203 K++ L+ L + L+I+++++G E T V+ D + +V I K E Sbjct: 168 NDKEE---LEFLLE----YVPNLIIQEFIEGQEYTVDVLCDLNGEVISIVPRK----RIE 216 Query: 204 LKYSSLNSTHVLPAKIPLDIYKEVQRLAFLAHQAIGCRGISRSDFLFDPLSRKVFWLEIN 263 ++ + + +++K +RLA +A+G RG + + EIN Sbjct: 217 VRAGETSKGVTVKDP---ELFKLAERLA----EALGARGPLNIQCFVTD--GEPYLFEIN 267 Query: 264 VQP---GMTPVSIFPEMAAYAGYSFRELLLWMVE 294 P G P+S AG + + ++ + Sbjct: 268 --PRFGGGYPLS------YMAGANEPDWIIRNLL 293 >gnl|CDD|162681 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions. Length = 864 Score = 39.4 bits (92), Expect = 0.001 Identities = 44/207 (21%), Positives = 83/207 (40%), Gaps = 32/207 (15%) Query: 10 SEREVSLSSGKA----CASALEDAGFKVSQ-------IDVDRSVG-----LVLAHLKPDL 53 S +V +G+ SA++D F + Q + D S+G +V K + Sbjct: 114 SHEQVGRYAGRLAVDLVRSAIDDGPFDLEQALQRLRDLVADASLGPSTAAIVDEAEKRGI 173 Query: 54 AFNVL-HGN---FGEDGLVQAILELLEIPYTHSGILASALSMDKMRSKQVVSSCGVPVCP 109 + L G+ G G Q ++ E T +A ++ DK +K+++S GVPV Sbjct: 174 PYMRLSAGSLVQLGY-GSRQKRIQATETDRT--SAIAVEIACDKDLTKEILSDAGVPVPE 230 Query: 110 SILVNRF--TMDSQHLISPPYVIKPLKGGSSLGI---IVIKKDQSIPLDLLQSSSWNHGD 164 +V ++ + P VIKP G G+ I+ + + + Sbjct: 231 GTVVQSAEDAWEAAQDLGYPVVIKPYDGNHGRGVTINILTRDEIESAYEAAV----EESS 286 Query: 165 QLLIEQYVDGIELTCGVMGDASLDVTE 191 +++E+++ G + V+G + V E Sbjct: 287 GVIVERFITGRDHRLLVVGGKVVAVAE 313 >gnl|CDD|162082 TIGR00877, purD, phosphoribosylamine--glycine ligase. This enzyme appears as a monofunctional protein in prokaryotes but as part of a larger, multidomain protein in eukaryotes. Length = 423 Score = 37.3 bits (87), Expect = 0.004 Identities = 35/136 (25%), Positives = 63/136 (46%), Gaps = 21/136 (15%) Query: 64 EDGLVQAILELLE---IPYTHSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDS 120 E LV +++ LE IP A+ L K +K + G+P + FT D Sbjct: 73 EAPLVLGLVDALEEAGIPVFGPTKEAAQLEGSKAFAKDFMKRYGIP---TAEYEVFT-DP 128 Query: 121 QHLIS-------PPYVIKP--LKGGSSLGIIVIK-KDQSIPL--DLLQSSSWNHGDQLLI 168 + +S P V+K L G G+IV K +++I ++L+ + G++++I Sbjct: 129 EEALSYIQEKGAPAIVVKADGLAAGK--GVIVAKTNEEAIKAVEEILEQKFGDAGERVVI 186 Query: 169 EQYVDGIELTCGVMGD 184 E+++DG E++ D Sbjct: 187 EEFLDGEEVSLLAFVD 202 >gnl|CDD|167327 PRK02186, PRK02186, argininosuccinate lyase; Provisional. Length = 887 Score = 36.0 bits (83), Expect = 0.011 Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 3/102 (2%) Query: 86 ASALSMDKMRSKQVVSSCGVPVCPSILVNRFT--MDSQHLISPPYVIKPLKGGSSLGIIV 143 A DK R + + G+ V + + +D+ ++ P V+KP G S+G+ + Sbjct: 101 AIRTCRDKKRLARTLRDHGIDVPRTHALALRAVALDALDGLTYPVVVKPRMGSGSVGVRL 160 Query: 144 IKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVMGDA 185 + L++ YV+G E + + A Sbjct: 161 CASVAEAA-AHCAALRRAGTRAALVQAYVEGDEYSVETLTVA 201 >gnl|CDD|180883 PRK07206, PRK07206, hypothetical protein; Provisional. Length = 416 Score = 35.8 bits (83), Expect = 0.015 Identities = 43/227 (18%), Positives = 71/227 (31%), Gaps = 65/227 (28%) Query: 16 LSSGKACASALEDAGFKVSQIDVDRSVGLVL----AHLKPDLAFNVLHGNFGEDGLVQAI 71 SSGK A A + G + + S L+ A V+ +G + + Sbjct: 11 FSSGKFLAPAFKKRGIEPIAV---TSSCLLDPYYYASFDTSDFIEVII-----NGDIDDL 62 Query: 72 LELLE-------IPYTHSGI-LASALS-----------------MDKMRSKQVVSSCGVP 106 +E L I SG+ LA L+ +K ++ G+P Sbjct: 63 VEFLRKLGPEAIIAGAESGVELADRLAEILTPQYSNDPALSSARRNKAEMINALAEAGLP 122 Query: 107 VCPSILVNRFT-----MDSQHLISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQ-SSSW 160 I + + LI P VIKPL+ S G+ + Sbjct: 123 AARQINTADWEEAEAWLRENGLIDRPVVIKPLESAGSDGVFICPAKGDWKHAFNAILGKA 182 Query: 161 NH----GDQLLIEQYVDGIELTCGVMGDASLDVTEIAVPKSDFYSYE 203 N + +L+++Y+ G TE V +F S + Sbjct: 183 NKLGLVNETVLVQEYLIG---------------TEYVV---NFVSLD 211 >gnl|CDD|179511 PRK02948, PRK02948, cysteine desulfurase; Provisional. Length = 381 Score = 34.7 bits (80), Expect = 0.027 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 8/68 (11%) Query: 13 EVSLSSGKACASALEDAGFKVSQIDVDRSVGLV-----LAHLKPDLAF-NVLHGNFGEDG 66 + +S + +LE G+ V++I VD+S GL+ + PD ++ H N E G Sbjct: 95 PMEHASIHSYFQSLESQGYTVTEIPVDKS-GLIRLVDLERAITPDTVLASIQHAN-SEIG 152 Query: 67 LVQAILEL 74 +Q I E+ Sbjct: 153 TIQPIAEI 160 >gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model describes DndA, a protein related to IscS and part of a larger family of cysteine desulfurases. It is encoded, typically, divergently from a conserved, sparsely distributed operon for sulfur modification of DNA. This modification system is designated dnd, after the phenotype of DNA degradation during electrophoresis. The system is sporadically distributed in bacteria, much like some restriction enzyme operons. DndB is described as a putative ATPase. Length = 353 Score = 34.0 bits (78), Expect = 0.044 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 6/60 (10%) Query: 23 ASALEDAGFKVSQIDVDRS----VGLVLAHLKPD-LAFNVLHGNFGEDGLVQAILELLEI 77 ALE GF V+ + VD S V + ++PD L +++H N E G +Q I E+ E+ Sbjct: 105 IRALERNGFTVTYLPVDESGRIDVDELADAIRPDTLLVSIMHVN-NETGSIQPIREIAEV 163 >gnl|CDD|184454 PRK14016, PRK14016, cyanophycin synthetase; Provisional. Length = 727 Score = 34.0 bits (79), Expect = 0.045 Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 17/105 (16%) Query: 81 HSGILASALSMDKMRSKQVVSSCGVPVCPSILVNRFTMDSQHL------ISPPYVIKPLK 134 + +A ++ DK +K+++++ GVPV +V ++ I P V+KPL Sbjct: 203 QTSAIAVDIACDKELTKRLLAAAGVPVPEGRVVT----SAEDAWEAAEEIGYPVVVKPLD 258 Query: 135 GGSSLGIIV-IKKDQSI--PLDLLQSSSWNHGDQLLIEQYVDGIE 176 G G+ V I + I + +++E+Y+ G + Sbjct: 259 GNHGRGVTVNITTREEIEAAYAVAS----KESSDVIVERYIPGKD 299 >gnl|CDD|132147 TIGR03103, trio_acet_GNAT, GNAT-family acetyltransferase TIGR03103. Members of this protein family belong to the GNAT family of acetyltransferases. 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 an asparagine synthetase family protein. Length = 547 Score = 30.9 bits (70), Expect = 0.41 Identities = 29/101 (28%), Positives = 50/101 (49%), Gaps = 12/101 (11%) Query: 85 LASALSM----DKMRSKQVVSSCGVPVCPSILVNRFTMDSQHLISP--PYVIKPLKGGSS 138 L SA++M DK ++++VS G+ V P + + ++ V+KP++G Sbjct: 286 LTSAVAMSLCDDKRLTRRLVSEAGLQV-PEQQLAGNGEAVEAFLAEHGAVVVKPVRGEQG 344 Query: 139 LGIIVIKKDQSIPLDLLQ--SSSWNHGDQLLIEQYVDGIEL 177 GI V D P DL + + D++L+E+YV G +L Sbjct: 345 KGISV---DVRTPDDLEAAIAKARQFCDRVLLERYVPGEDL 382 >gnl|CDD|162020 TIGR00747, fabH, 3-oxoacyl-(acyl-carrier-protein) synthase III. Active site residues include Cys112, His244 and Asn274 of E. coli FabH. Cys-112 is the site of acyl group attachment. Length = 318 Score = 30.8 bits (70), Expect = 0.47 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 6/49 (12%) Query: 8 ISSEREVSLSSG-KACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAF 55 I+++ E S + G +A A+E+AG ID +++A PD AF Sbjct: 44 IAADDETSSTMGFEAAKRAIENAGISKDDID-----LIIVATTTPDHAF 87 >gnl|CDD|162798 TIGR02291, rimK_rel_E_lig, alpha-L-glutamate ligase-related protein. Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (TIGR00768), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown. Length = 317 Score = 30.2 bits (68), Expect = 0.66 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%) Query: 92 DKMRSKQVVSSCG--VPVCPSILVNRFTMDSQHLI---SPPYVIKPLKGGSSLGIIVI 144 DK+++K + + G VP ++ N+ + + H I P +VIKP +G GI+VI Sbjct: 37 DKLKTKIIAQAAGITVPELYGVIHNQAEVKTIHNIVKDHPDFVIKPAQGSGGKGILVI 94 >gnl|CDD|177971 PLN02337, PLN02337, lipoxygenase. Length = 866 Score = 30.0 bits (68), Expect = 0.82 Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 9/40 (22%) Query: 147 DQSIPLDLL------QSSSWNHGDQLLIEQY---VDGIEL 177 +Q++P DL+ + S HG +LLIE Y VDG+E+ Sbjct: 601 EQALPADLIKRGVAVEDPSSPHGVRLLIEDYPYAVDGLEI 640 >gnl|CDD|180150 PRK05586, PRK05586, biotin carboxylase; Validated. Length = 447 Score = 29.7 bits (67), Expect = 1.1 Identities = 19/94 (20%), Positives = 44/94 (46%), Gaps = 16/94 (17%) Query: 92 DKMRSKQVVSSCGVPVCP----SILVNRFTMDSQHLISPPYVIKPLKGGSSLGIIVIKKD 147 +K +++++ GVPV P I ++ I P ++K GG GI +++ + Sbjct: 115 NKSNAREIMIKAGVPVVPGSEGEIENEEEALEIAKEIGYPVMVKASAGGGGRGIRIVRSE 174 Query: 148 QSIPLDLLQS-------SSWNHGD-QLLIEQYVD 173 + +L+++ + GD + IE++++ Sbjct: 175 E----ELIKAFNTAKSEAKAAFGDDSMYIEKFIE 204 >gnl|CDD|132443 TIGR03402, FeS_nifS, cysteine desulfurase NifS. Members of this protein family are NifS, one of several related families of cysteine desulfurase involved in iron-sulfur (FeS) cluster biosynthesis. NifS is part of the NIF system, usually associated with other nif genes involved in nitrogenase expression and nitrogen fixation. The protein family is given a fairly broad interpretation here. It includes a clade nearly always found in extended nitrogen fixation genomic regions, plus a second clade more closely related to the first than to IscS and also part of NifS-like/NifU-like systems. This model does not extend to a more distantly clade found in the epsilon proteobacteria such as Helicobacter pylori, also named NifS in the literature, built instead in TIGR03403. Length = 379 Score = 28.7 bits (65), Expect = 1.8 Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 6/57 (10%) Query: 26 LEDAGFKVSQIDVDRSVGLVLAHLK----PDLAF-NVLHGNFGEDGLVQAILELLEI 77 LE G+KV+ + VD L L L+ D A +V+ N E G + I E+ EI Sbjct: 106 LEKQGYKVTYLPVDEEGRLDLEELRAAITDDTALVSVMWAN-NETGTIFPIEEIGEI 161 >gnl|CDD|179527 PRK03011, PRK03011, butyrate kinase; Provisional. Length = 358 Score = 28.6 bits (65), Expect = 1.8 Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 11/43 (25%) Query: 242 GISRSDFLFDPLSRKVFWLEINVQPGMTPVSIFP---EMAAYA 281 G++ S L + + +V ++ PV ++P EM A A Sbjct: 304 GLAYSKRLVERIKERVSFI--------APVIVYPGEDEMEALA 338 >gnl|CDD|178963 PRK00290, dnaK, molecular chaperone DnaK; Provisional. Length = 627 Score = 28.5 bits (65), Expect = 2.0 Identities = 10/16 (62%), Positives = 11/16 (68%) Query: 22 CASALEDAGFKVSQID 37 C AL+DAG VS ID Sbjct: 313 CKQALKDAGLSVSDID 328 >gnl|CDD|180313 PRK05928, hemD, uroporphyrinogen-III synthase; Reviewed. Length = 249 Score = 28.8 bits (65), Expect = 2.0 Identities = 20/73 (27%), Positives = 26/73 (35%), Gaps = 9/73 (12%) Query: 19 GKACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFN----VLHGNFG----EDGLVQA 70 G+ A AL+ G KV + D +L L L L GN G D L + Sbjct: 88 GEKTALALKKLGGKVVFVPEDGESSELLLELPELLLKGKRVLYLRGNGGREVLGDTLEER 147 Query: 71 ILELLE-IPYTHS 82 E+ E Y Sbjct: 148 GAEVDECEVYERV 160 >gnl|CDD|181436 PRK08462, PRK08462, biotin carboxylase; Validated. Length = 445 Score = 28.2 bits (63), Expect = 2.6 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 4/78 (5%) Query: 86 ASALSMDKMRSKQVVSSCGVPVCP-SILVNRFTMDSQHL---ISPPYVIKPLKGGSSLGI 141 AL DK ++K+V+ GVPV P S + +++ + I P ++K GG G+ Sbjct: 111 VMALMSDKSKAKEVMKRAGVPVIPGSDGALKSYEEAKKIAKEIGYPVILKAAAGGGGRGM 170 Query: 142 IVIKKDQSIPLDLLQSSS 159 V++ + + L + S Sbjct: 171 RVVEDESDLENLYLAAES 188 >gnl|CDD|181732 PRK09258, PRK09258, 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed. Length = 338 Score = 28.3 bits (64), Expect = 2.7 Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 7/66 (10%) Query: 4 LMGGISSER----EVSLSSG--KACASALEDAGFKVSQIDVDRSVGLVLAHLKPDLAFNV 57 + GI R LS G A AL +AG S I + + + +L+P A V Sbjct: 45 ALTGIRERRWWPEGTQLSDGAIAAGRKALAEAGIDPSDIGLLINTSVCRDYLEPATACRV 104 Query: 58 LHGNFG 63 H N G Sbjct: 105 -HHNLG 109 >gnl|CDD|173003 PRK14537, PRK14537, 50S ribosomal protein L20/unknown domain fusion protein; Provisional. Length = 230 Score = 28.0 bits (62), Expect = 3.0 Identities = 9/23 (39%), Positives = 17/23 (73%) Query: 30 GFKVSQIDVDRSVGLVLAHLKPD 52 G ++++D++R V LAHL+P+ Sbjct: 82 GLALAKVDINRKVLSDLAHLQPE 104 >gnl|CDD|183765 PRK12815, carB, carbamoyl phosphate synthase large subunit; Reviewed. Length = 1068 Score = 27.2 bits (61), Expect = 5.8 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 12/73 (16%) Query: 123 LISPPYVIKPLKGGSSLGIIVIKKDQSIPLDLLQSSSWNHGDQLLIEQYVDGIELTCGVM 182 LI P YVI GG G+ V+ + ++ L +++S + +LI+Q++DG E Sbjct: 709 LIRPSYVI----GG--QGMAVVYDEPALEAYLAENASQLY--PILIDQFIDGKEYEV--- 757 Query: 183 GDASLDVTEIAVP 195 DA D ++ +P Sbjct: 758 -DAISDGEDVTIP 769 >gnl|CDD|162895 TIGR02510, NrdE-prime, ribonucleoside-diphosphate reductase, alpha chain. This model represents a small clade of ribonucleoside-diphosphate reductase, alpha chains which are sufficiently divergent from the usual Class I RNR alpha chains (NrdE or NrdA, TIGR02506) as to warrant their own model. The genes from Thermus thermophilus, Dichelobacter and Salinibacter are adjacent to the usual RNR beta chain. Length = 571 Score = 26.9 bits (59), Expect = 7.2 Identities = 12/24 (50%), Positives = 14/24 (58%) Query: 190 TEIAVPKSDFYSYELKYSSLNSTH 213 TEIA+P D S+ SSLN H Sbjct: 263 TEIALPSDDEESFTCCLSSLNLLH 286 >gnl|CDD|184035 PRK13406, bchD, magnesium chelatase subunit D; Provisional. Length = 584 Score = 26.5 bits (59), Expect = 8.4 Identities = 14/42 (33%), Positives = 20/42 (47%) Query: 7 GISSEREVSLSSGKACASALEDAGFKVSQIDVDRSVGLVLAH 48 GI+S R L+ A A+A V + D+ + LVLA Sbjct: 212 GIASLRAPLLALRAARAAAALAGRTAVEEEDLALAARLVLAP 253 >gnl|CDD|179724 PRK04040, PRK04040, adenylate kinase; Provisional. Length = 188 Score = 26.4 bits (59), Expect = 9.5 Identities = 7/14 (50%), Positives = 10/14 (71%) Query: 218 KIPLDIYKEVQRLA 231 K+P + KE+QR A Sbjct: 57 KLPPEEQKELQREA 70 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 0.320 0.137 0.401 Gapped Lambda K H 0.267 0.0772 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,879,593 Number of extensions: 305748 Number of successful extensions: 678 Number of sequences better than 10.0: 1 Number of HSP's gapped: 631 Number of HSP's successfully gapped: 40 Length of query: 300 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 207 Effective length of database: 3,984,929 Effective search space: 824880303 Effective search space used: 824880303 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 (21.8 bits) S2: 57 (25.7 bits)