Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate PP_2375 PP_2375 cobalamin-dependent methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >FitnessBrowser__Putida:PP_2375 Length = 1235 Score = 1607 bits (4160), Expect = 0.0 Identities = 821/1235 (66%), Positives = 978/1235 (79%), Gaps = 14/1235 (1%) Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61 S++++ L+ L ERIL+LDGGMGTMIQSYRL E D+RG RFADWP D+KGNNDLL+LS+P Sbjct: 5 SARLQALQNALKERILILDGGMGTMIQSYRLEEHDYRGTRFADWPSDVKGNNDLLLLSRP 64 Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121 +VIAAI AY +AGADI+ETNTFN+T I+ ADY MESL E+N A++AR AD T Sbjct: 65 DVIAAIEKAYLDAGADILETNTFNATQISQADYGMESLVYELNVEGARIARQVADAKTLE 124 Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181 TP+KPR+VAGVLGPT+RT SISPDVNDP FRN+TFD LV Y E+T+ L+EGGADLILIE Sbjct: 125 TPDKPRFVAGVLGPTSRTCSISPDVNDPGFRNVTFDELVENYIEATRGLIEGGADLILIE 184 Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241 T+FDTLNAKAA+FAV+ FE VELPIMISGTITDASGRTLSGQTTEAF+NS+RHA+ + Sbjct: 185 TIFDTLNAKAAIFAVQQVFEDDNVELPIMISGTITDASGRTLSGQTTEAFWNSVRHAKPI 244 Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301 + GLNCALG +LR Y++EL+ A+ +V+AHPNAGLPNAFGEYD MA + E+A + Sbjct: 245 SVGLNCALGAKDLRPYLEELATKADTHVSAHPNAGLPNAFGEYDETPAEMAAVVEEFAAS 304 Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361 GFLNI+GGCCGTTP HI A++ AV PR++PEI ACRLSGLEP I SLFVNVGE Sbjct: 305 GFLNIIGGCCGTTPGHIQAIAEAVAKYKPREIPEIAKACRLSGLEPFTIDRQSLFVNVGE 364 Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421 RTN+TGSAKF RLI+EE Y+EAL+VA QQVE GAQ+IDINMDEGMLD++AAMVRFLNLIA Sbjct: 365 RTNITGSAKFARLIREENYTEALEVALQQVEAGAQVIDINMDEGMLDSQAAMVRFLNLIA 424 Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481 GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ F HHA+L +RYGAAVV Sbjct: 425 GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFKHHARLCKRYGAAVV 484 Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541 VMAFDE GQADT ARK EIC+R+Y IL EVGFPPEDIIFDPNIFAVATGIEEHNNYA D Sbjct: 485 VMAFDEVGQADTAARKKEICQRSYDILVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVD 544 Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601 FI AC I+ LPHAL SGGVSNVSFSFRGN+PVREAIH+VFLY+AI+NG+ MGIVNAGQ Sbjct: 545 FIEACAYIRDHLPHALSSGGVSNVSFSFRGNNPVREAIHSVFLYHAIQNGLTMGIVNAGQ 604 Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661 L IYD++PA+LR+ VEDV+LNR GT+ LL +A+ Y+G T + EWRS V K Sbjct: 605 LEIYDEIPAQLREKVEDVVLNRTPHGTDALLAIADDYKGGGA--TKEVENEEWRSLPVEK 662 Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721 RLE++LVKGIT FI +DTE RQQ RPIEVIEGPLM+GMNVVGDLFG GKMFLPQVVKS Sbjct: 663 RLEHALVKGITAFIVEDTEACRQQCARPIEVIEGPLMNGMNVVGDLFGAGKMFLPQVVKS 722 Query: 722 ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780 ARVMKQAVA+L PFIEA K ++ + GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVDL Sbjct: 723 ARVMKQAVAHLIPFIEAEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDL 782 Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840 GVMVPAEKIL+TA+E D+IGLSGLITPSLDEMV+VA+EM+RQGF +PL+IGGATTSKA Sbjct: 783 GVMVPAEKILQTAREQKCDIIGLSGLITPSLDEMVHVAREMQRQGFELPLMIGGATTSKA 842 Query: 841 HTAVKIEQNYSGPTV-YVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899 HTAVKIE YS V YV +ASR VGV LLS + FV +TR EY VR + + Sbjct: 843 HTAVKIEPKYSNDAVIYVTDASRAVGVATQLLSKELKPGFVEKTRLEYVDVRERTANRSA 902 Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958 RT ++ A +DW Y P GV+ +E + TL YIDWTPFF++W LAG Sbjct: 903 RTERLSYAQAIAAKPQYDWAGYQPTAPSFTGVKVLEDIDLRTLAEYIDWTPFFISWDLAG 962 Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017 K+PRIL DEVVG A L+KDA +MLDKL EK ++ R V G +PAN+V DDIE+Y ++ Sbjct: 963 KFPRILTDEVVGEAATALYKDAREMLDKLIDEKLISARAVFGFWPANQVDDDDIEVYGED 1022 Query: 1018 TRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076 + + HHLRQQT K G N+ LADFVAPK SG DY+G F T G+ + +A A+ Sbjct: 1023 GQ--ALATLHHLRQQTIKPDGKPNWSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAY 1080 Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136 + + DDY+ IMVKALADRLAEA AE+LHE+VRK +WGYA +E+L NE LI+E Y GIRPA Sbjct: 1081 QDKGDDYSSIMVKALADRLAEACAEWLHEQVRKEHWGYARDEHLDNEALIKEQYSGIRPA 1140 Query: 1137 PGYPACPEHTEKATIWELLE-----VEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYA 1191 PGYPACP+HTEK T++ LL+ +G+ LTE FAM+P A+VSGWYF+HP +KY+A Sbjct: 1141 PGYPACPDHTEKETLFRLLDGTAIGETGPSGVYLTEHFAMFPAAAVSGWYFAHPQAKYFA 1200 Query: 1192 VAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDA 1226 V ++ +DQ+E Y+ RKG ++ ERWLAPNLGYD+ Sbjct: 1201 VGKVDKDQIERYSARKGQDISVSERWLAPNLGYDS 1235 Lambda K H 0.318 0.134 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 3851 Number of extensions: 160 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 1227 Length of database: 1235 Length adjustment: 47 Effective length of query: 1180 Effective length of database: 1188 Effective search space: 1401840 Effective search space used: 1401840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 59 (27.3 bits)
Align candidate PP_2375 PP_2375 (cobalamin-dependent methionine synthase)
to HMM TIGR02082 (metH: methionine synthase (EC 2.1.1.13))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR02082.hmm # target sequence database: /tmp/gapView.6897.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02082 [M=1182] Accession: TIGR02082 Description: metH: methionine synthase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1766.9 0.0 0 1766.7 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_2375 PP_2375 cobalamin-dependent meth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_2375 PP_2375 cobalamin-dependent methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1766.7 0.0 0 0 1 1182 [] 15 1201 .. 15 1201 .. 0.98 Alignments for each domain: == domain 1 score: 1766.7 bits; conditional E-value: 0 TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72 l++ril+lDG+mGt++qs++L+e+d+rg +ad+++++kGnndlL l++P+viaai +ay++aGaDi+etntF lcl|FitnessBrowser__Putida:PP_2375 15 LKERILILDGGMGTMIQSYRLEEHDYRGTrFADWPSDVKGNNDLLLLSRPDVIAAIEKAYLDAGADILETNTF 87 579********************************************************************** PP TIGR02082 73 nsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtyd 144 n+t+i++adY++e+++yeln ++a++ar+vad t tp+k+RfvaG+lGPt+++ ++spdv++p+frnvt+d lcl|FitnessBrowser__Putida:PP_2375 88 NATQISQADYGMESLVYELNVEGARIARQVADAKTlETPDKPRFVAGVLGPTSRTCSISPDVNDPGFRNVTFD 160 *********************************99899*********************************** PP TIGR02082 145 elvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtlea 217 elv+ Y e+++gl++GG+Dl+Liet+fDtlnakaa+fav++vfe+ ++elPi+isg+i+d+sGrtLsGqt+ea lcl|FitnessBrowser__Putida:PP_2375 161 ELVENYIEATRGLIEGGADLILIETIFDTLNAKAAIFAVQQVFEDDNVELPIMISGTITDASGRTLSGQTTEA 233 ************************************************************************* PP TIGR02082 218 flaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegl 290 f +s++ha+ +++GLnCalGa++lr++++el+ +a++ vs++PnaGLPna+geYd+tp e+a++++efa+ g+ lcl|FitnessBrowser__Putida:PP_2375 234 FWNSVRHAKPISVGLNCALGAKDLRPYLEELATKADTHVSAHPNAGLPNAFGEYDETPAEMAAVVEEFAASGF 306 ************************************************************************* PP TIGR02082 291 lnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklik 363 lni+GGCCGttP hi+aiaeav++ kpr+ +e+ ++++lsgle+++i+++s fvn+GeRtn++Gs+kf++li+ lcl|FitnessBrowser__Putida:PP_2375 307 LNIIGGCCGTTPGHIQAIAEAVAKYKPREIPEIAKACRLSGLEPFTIDRQSLFVNVGERTNITGSAKFARLIR 379 ************************************************************************* PP TIGR02082 364 aedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviq 436 +e+y eal++a qqve Gaq++Din+De++lD++a+m+++l+l+a+epdi++vP+m+Dss++ev+eaGLk+iq lcl|FitnessBrowser__Putida:PP_2375 380 EENYTEALEVALQQVEAGAQVIDINMDEGMLDSQAAMVRFLNLIAGEPDISRVPIMIDSSKWEVIEAGLKCIQ 452 ************************************************************************* PP TIGR02082 437 GkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifD 509 Gk+ivnsis+k+G+e+F ++a+l k+yGaavvvmafDe Gqa+ta++k ei++R y++l+++vgfppediifD lcl|FitnessBrowser__Putida:PP_2375 453 GKGIVNSISMKEGVEQFKHHARLCKRYGAAVVVMAFDEVGQADTAARKKEICQRSYDILVNEVGFPPEDIIFD 525 ************************************************************************* PP TIGR02082 510 pniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmg 582 pni+++atGieeh++ya+dfiea+ i+ +lP+a sgGvsnvsFs+rgn++vRea+hsvFLy+ai++Gl mg lcl|FitnessBrowser__Putida:PP_2375 526 PNIFAVATGIEEHNNYAVDFIEACAYIRDHLPHALSSGGVSNVSFSFRGNNPVREAIHSVFLYHAIQNGLTMG 598 ************************************************************************* PP TIGR02082 583 ivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralv 655 ivnag+l++yd+i+++lre+ved++l+r ++ t+ Ll +a+ ykg ++ ke +++ewr+lpve+RLe+alv lcl|FitnessBrowser__Putida:PP_2375 599 IVNAGQLEIYDEIPAQLREKVEDVVLNRTPHGTDALLAIADDYKGGGAT--KEVENEEWRSLPVEKRLEHALV 669 *********************************************9999..8999****************** PP TIGR02082 656 kGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekeke 728 kG++ +i ed+e+ r++ +p+e+iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+ek lcl|FitnessBrowser__Putida:PP_2375 670 KGITAFIVEDTEACRQQCARPIEVIEGPLMNGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIEAEKG 742 ************************************************************************8 PP TIGR02082 729 ed.kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivkslde 800 ++ ++kGki++atvkGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++a+++k D+iglsGLi++slde lcl|FitnessBrowser__Putida:PP_2375 743 DKpEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQTAREQKCDIIGLSGLITPSLDE 815 87689******************************************************************** PP TIGR02082 801 mvevaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkkaeelekike 872 mv+va+em+r+g+++Pl++GGa++skah+avki++kY+ v+yv+das+av v+ +lls++ k ++ek++ lcl|FitnessBrowser__Putida:PP_2375 816 MVHVAREMQRQGFELPLMIGGATTSKAHTAVKIEPKYSNdAVIYVTDASRAVGVATQLLSKELKPGFVEKTRL 888 *************************************872599****************************** PP TIGR02082 873 eyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWel 944 ey ++re+ ++ +++ ls ++a + + d+ ++++ap f G+kvle++ + +l +yiDw+++F++W+l lcl|FitnessBrowser__Putida:PP_2375 889 EYVDVRERTANRSARTERLSYAQAIAAKPQYDWA-GYQPTAPSFTGVKVLEDIdLRTLAEYIDWTPFFISWDL 960 **********************************.9************************************* PP TIGR02082 945 rgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddieiytdetvsqetkpiat 1016 +gk+p+il+de++g+ a+ l+kda+e+ldkl+ ekl+ ar+v+G++Pa++v+ ddie+y +++ +at lcl|FitnessBrowser__Putida:PP_2375 961 AGKFPRILTDEVVGEAATALYKDAREMLDKLIDEKLISARAVFGFWPANQVDdDDIEVYGEDGQ-----ALAT 1028 ************************************************9875268*****8776.....6677 PP TIGR02082 1017 vrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlae 1088 +++ ++q+ + ++ + +laDf+a+k+sG +Dy+g +++tag+gaee ak++++k ddy+si+vkaladrlae lcl|FitnessBrowser__Putida:PP_2375 1029 LHHLRQQTIKPDGKpNWSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAYQDKGDDYSSIMVKALADRLAE 1101 666555555555556********************************************************** PP TIGR02082 1089 alaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaeri......Glkl 1155 a ae+lhe+vRke+wgya++e+ld+e l+ke+Y Girpa+GYpacPdhtek tl++Ll+ i G++l lcl|FitnessBrowser__Putida:PP_2375 1102 ACAEWLHEQVRKEHWGYARDEHLDNEALIKEQYSGIRPAPGYPACPDHTEKETLFRLLDGTAIgetgpsGVYL 1174 **********************************************************987663333337*** PP TIGR02082 1156 teslalaPeasvsglyfahpeakYfav 1182 te +a+ P+a+vsg+yfahp+akYfav lcl|FitnessBrowser__Putida:PP_2375 1175 TEHFAMFPAAAVSGWYFAHPQAKYFAV 1201 *************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1235 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.11u 0.05s 00:00:00.16 Elapsed: 00:00:00.15 # Mc/sec: 9.60 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory