Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_077243567.1 B1A74_RS01430 methionine synthase
Query= CharProtDB::CH_090726 (1227 letters) >NCBI__GCF_001995255.1:WP_077243567.1 Length = 1263 Score = 1655 bits (4287), Expect = 0.0 Identities = 820/1247 (65%), Positives = 988/1247 (79%), Gaps = 24/1247 (1%) Query: 1 MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60 M++ + + L ERIL+LDGGMGT IQ Y L EAD+RGERF DW DLKGNNDLL L++ Sbjct: 1 MTATRQDIENALKERILILDGGMGTTIQLYELGEADYRGERFKDWESDLKGNNDLLSLTR 60 Query: 61 PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120 P++I IHN Y EAGADIIE NTFN T IAMADY ME L E+N +AKLAR AD WTA Sbjct: 61 PDIIEQIHNDYLEAGADIIEANTFNGTRIAMADYHMEDLVPELNRESAKLARKAADAWTA 120 Query: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180 +TP+KPR+VAG+LGPTNRTASISPDVNDP RN+ FD LVAAY+E+ +AL+EGG DL+LI Sbjct: 121 KTPDKPRFVAGILGPTNRTASISPDVNDPGARNVDFDTLVAAYKEAAEALIEGGVDLLLI 180 Query: 181 ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240 ETVFDTLNAKAA+FAVKT + LG +LPIMISGTITDASGRTLSGQTTEAF+NS+RHA Sbjct: 181 ETVFDTLNAKAAIFAVKTLEDELGKDLPIMISGTITDASGRTLSGQTTEAFWNSVRHANP 240 Query: 241 LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300 ++ GLNCALG E+RQYV+ELSRIA+ +V+AHPNAGLPN FG+YD + MA + WA+ Sbjct: 241 VSIGLNCALGAKEMRQYVEELSRIADTHVSAHPNAGLPNEFGDYDESPEQMAADVGPWAE 300 Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360 G LNI+GGCCGT P+HI AM AVE PRK+PE+ ACRLSGLEP NI +DSLFVNVG Sbjct: 301 QGMLNIIGGCCGTLPEHIRAMREAVEKFPPRKVPEVSPACRLSGLEPCNITDDSLFVNVG 360 Query: 361 ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420 ERTNVTGS KF RLI+ E+Y AL+VA QVE GAQIID+NMDEGML+++ AMVRFLNL+ Sbjct: 361 ERTNVTGSRKFLRLIQNEEYDVALEVALNQVEGGAQIIDVNMDEGMLESQDAMVRFLNLL 420 Query: 421 AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480 AGEPDIARVP+MIDSSK+++IE GLKC+QGK +VNSISMKEG + FI A+L RRYGAA+ Sbjct: 421 AGEPDIARVPVMIDSSKFEIIEAGLKCVQGKPVVNSISMKEGEENFIKQAELCRRYGAAI 480 Query: 481 VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540 VVMAFDE GQAD R++EIC RAYK+LTE+VGFP EDIIFDPNIFAVATGIEEHNNY Sbjct: 481 VVMAFDEDGQADNEQRRVEICTRAYKLLTEKVGFPAEDIIFDPNIFAVATGIEEHNNYGV 540 Query: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600 DFI A IK +LPHALISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAG Sbjct: 541 DFIEATRRIKNDLPHALISGGVSNVSFSFRGNEPVREAIHAVFLYHAIKAGMDMGIVNAG 600 Query: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660 QLA+YDD+ +L++AVEDV+LNRRDD T+RLLEL+E+Y+G + EWR WEV+ Sbjct: 601 QLAVYDDIDEKLKEAVEDVVLNRRDDATDRLLELSEEYKGQ--GGGKKEENLEWREWEVS 658 Query: 661 KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720 KRLE+SLVKGI ++ DTEEARQ RPI+VIEGPLMDGMNVVGDLFGEGKMFLPQVVK Sbjct: 659 KRLEHSLVKGIDTYVVDDTEEARQAYDRPIQVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 718 Query: 721 SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780 SARVMK+AVA+L P+IEA K + NGK+++ATVKGDVHDIGKNIVGVVLQCNN+E++D+ Sbjct: 719 SARVMKKAVAHLIPYIEAEKTGTENNGKILMATVKGDVHDIGKNIVGVVLQCNNFEVIDI 778 Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840 GVM P +IL+ AKE + D+IGLSGLITPSL+EM N A ++ER+G T PL+IGGATTS+A Sbjct: 779 GVMQPGAEILKAAKEHDVDVIGLSGLITPSLEEMANFAADLEREGMTTPLMIGGATTSRA 838 Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900 HTAVKIE NYSGP V+V++ASR VGV +L+S R+++ A R+EYE +R+Q+ +K + Sbjct: 839 HTAVKIEPNYSGPVVWVKDASRAVGVAQSLISPELRENYAAEIREEYEKLRVQNAGRKKK 898 Query: 901 TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV--------------------EASIET 940 ++LE AR N DW AY P L +++ + + Sbjct: 899 VQWLSLEKARANKPEIDWSAYAPAKPKALETEDLPGEPTVLHPHGDGSVLLRFDDFDLNK 958 Query: 941 LRNYIDWTPFFMTWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVG 1000 ++ YIDWTPFF +W L YPRILEDE VG EA++LFKD +ML ++ EK + RGVVG Sbjct: 959 VKEYIDWTPFFHSWQLHAAYPRILEDEKVGEEARKLFKDGQEMLQRMIDEKWVTCRGVVG 1018 Query: 1001 LFPANRVG-DDIEIYRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYI 1058 FPAN V DDIE+Y DE R+ V+ HHLRQQTEK G ++ LADFV PK +G DYI Sbjct: 1019 FFPANSVDHDDIEVYTDENRSQVLKKLHHLRQQTEKRRGQPSHSLADFVMPKEAGGPDYI 1078 Query: 1059 GAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNE 1118 GAFAV+ G + DA A+ +E +DDY+ I+VK+LADRLAEAFAE +HE VRK YWGY +E Sbjct: 1079 GAFAVSAGGDVDAKAEEYEKANDDYHAILVKSLADRLAEAFAECMHEYVRKYYWGYVADE 1138 Query: 1119 NLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVS 1178 L NE+LI E YQGIRPAPGYPACPEHTEKAT+WELL+ E++ M LTES+AM P ++VS Sbjct: 1139 QLENEDLIEEKYQGIRPAPGYPACPEHTEKATLWELLQAEENADMTLTESYAMLPVSAVS 1198 Query: 1179 GWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225 GWYF+HP+S+Y+ + ++ RDQVEDYA+RKGMS E ERWLAPN+GYD Sbjct: 1199 GWYFAHPESRYFGLGKVNRDQVEDYAKRKGMSFEEAERWLAPNIGYD 1245 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: 3925 Number of extensions: 158 Number of successful extensions: 5 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: 1263 Length adjustment: 48 Effective length of query: 1179 Effective length of database: 1215 Effective search space: 1432485 Effective search space used: 1432485 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 WP_077243567.1 B1A74_RS01430 (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.3022210.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 1765.7 0.0 0 1765.4 0.0 1.0 1 NCBI__GCF_001995255.1:WP_077243567.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001995255.1:WP_077243567.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1765.4 0.0 0 0 1 1181 [. 12 1211 .. 12 1212 .. 0.98 Alignments for each domain: == domain 1 score: 1765.4 bits; conditional E-value: 0 TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetn 70 l++ril+lDG+mGt++q ++L ead+rge ++d++++lkGnndlL+lt+P++i++ih++y+eaGaDi+e n NCBI__GCF_001995255.1:WP_077243567.1 12 LKERILILDGGMGTTIQLYELGEADYRGErFKDWESDLKGNNDLLSLTRPDIIEQIHNDYLEAGADIIEAN 82 579******************************************************************** PP TIGR02082 71 tFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrn 140 tFn+t ia+adY++ed++ eln+++aklar++ad +t +tp+k+RfvaG lGPtn++a++spdv++p+ rn NCBI__GCF_001995255.1:WP_077243567.1 83 TFNGTRIAMADYHMEDLVPELNRESAKLARKAADAWTaKTPDKPRFVAGILGPTNRTASISPDVNDPGARN 153 *********************************************************************** PP TIGR02082 141 vtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLs 211 v++d+lv+aYke++++l++GGvDllLietvfDtlnakaa+fav+++ +e g++lPi+isg+i+d+sGrtLs NCBI__GCF_001995255.1:WP_077243567.1 154 VDFDTLVAAYKEAAEALIEGGVDLLLIETVFDTLNAKAAIFAVKTLEDELGKDLPIMISGTITDASGRTLS 224 *********************************************************************** PP TIGR02082 212 GqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakal 282 Gqt+eaf +s++ha+ +++GLnCalGa+e+r++v+els++a++ vs++PnaGLPn++g+Yd+ pe++a+ + NCBI__GCF_001995255.1:WP_077243567.1 225 GQTTEAFWNSVRHANPVSIGLNCALGAKEMRQYVEELSRIADTHVSAHPNAGLPNEFGDYDESPEQMAADV 295 *********************************************************************** PP TIGR02082 283 kefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnva 353 +ae+g+lni+GGCCGt Pehira+ eav++ prk++e+ ++++lsgle+ +i+++s fvn+GeRtnv+ NCBI__GCF_001995255.1:WP_077243567.1 296 GPWAEQGMLNIIGGCCGTLPEHIRAMREAVEKFPPRKVPEVSPACRLSGLEPCNITDDSLFVNVGERTNVT 366 *********************************************************************** PP TIGR02082 354 GskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDsse 424 Gs+kf +li++e+y+ al++a +qve Gaqi+D+n+De++l+++ +m+++l+lla+epdia+vP+m+Dss+ NCBI__GCF_001995255.1:WP_077243567.1 367 GSRKFLRLIQNEEYDVALEVALNQVEGGAQIIDVNMDEGMLESQDAMVRFLNLLAGEPDIARVPVMIDSSK 437 *********************************************************************** PP TIGR02082 425 fevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykll 495 fe++eaGLk++qGk +vnsis+k+Gee+F+++a+l ++yGaa+vvmafDe+Gqa++ ++++ei++Raykll NCBI__GCF_001995255.1:WP_077243567.1 438 FEIIEAGLKCVQGKPVVNSISMKEGEENFIKQAELCRRYGAAIVVMAFDEDGQADNEQRRVEICTRAYKLL 508 *********************************************************************** PP TIGR02082 496 tekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavReal 566 tekvgfp+ediifDpni+++atGieeh++y++dfiea+r+ik++lP+a isgGvsnvsFs+rgn++vRea+ NCBI__GCF_001995255.1:WP_077243567.1 509 TEKVGFPAEDIIFDPNIFAVATGIEEHNNYGVDFIEATRRIKNDLPHALISGGVSNVSFSFRGNEPVREAI 579 *********************************************************************** PP TIGR02082 567 hsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaq 637 h+vFLy+aikaG+Dmgivnag+lavyddid+ l+e+ved++l+rr++at++Llel e ykg+ k+++ NCBI__GCF_001995255.1:WP_077243567.1 580 HAVFLYHAIKAGMDMGIVNAGQLAVYDDIDEKLKEAVEDVVLNRRDDATDRLLELSEEYKGQGGG--KKEE 648 **************************************************************999..7789 PP TIGR02082 638 eaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvks 708 + ewr+++v++RLe++lvkG+ ++ +d+eear+ + +p+++iegpL+dGm+vvGdLFG+GkmfLPqvvks NCBI__GCF_001995255.1:WP_077243567.1 649 NLEWREWEVSKRLEHSLVKGIDTYVVDDTEEARQAYDRPIQVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 719 99********************************************************************* PP TIGR02082 709 arvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekilea 779 arvmkkava+L+Py+e+ek+ ++++Gki++atvkGDvhDiGkniv+vvL+cn++ev+d+Gv++P ++il+a NCBI__GCF_001995255.1:WP_077243567.1 720 ARVMKKAVAHLIPYIEAEKTGTENNGKILMATVKGDVHDIGKNIVGVVLQCNNFEVIDIGVMQPGAEILKA 790 *********************************************************************** PP TIGR02082 780 akkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdasea 850 ak+++ DviglsGLi++sl+em++ a ++er+g+++Pl++GGa++s+ah+avki+++Y+g+vv+vkdas+a NCBI__GCF_001995255.1:WP_077243567.1 791 AKEHDVDVIGLSGLITPSLEEMANFAADLEREGMTTPLMIGGATTSRAHTAVKIEPNYSGPVVWVKDASRA 861 *********************************************************************** PP TIGR02082 851 vkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrse.............. 907 v v+++l+s + +++++++i+eeye++r + +k+k++ ls+++ar ++ ++d+s NCBI__GCF_001995255.1:WP_077243567.1 862 VGVAQSLISPELRENYAAEIREEYEKLRVQNAGRKKKVQWLSLEKARANKPEIDWSAyapakpkaletedl 932 ********************************************************999999999999988 PP TIGR02082 908 ..dlevpapkflGtkvleas...ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelld 973 + +v +p+ G+ l+ ++++ +yiDw+++F +W+l+ yp+il+de++g+earklfkd +e+l+ NCBI__GCF_001995255.1:WP_077243567.1 933 pgEPTVLHPHGDGSVLLRFDdfdLNKVKEYIDWTPFFHSWQLHAAYPRILEDEKVGEEARKLFKDGQEMLQ 1003 88888888999998877644459************************************************ PP TIGR02082 974 klsaekllrargvvGlfPaqsv.gddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaske 1042 +++ ek +++rgvvG+fPa+sv +ddie+ytde +sq k++ +r +q+++ +++ +laDf+ +ke NCBI__GCF_001995255.1:WP_077243567.1 1004 RMIDEKWVTCRGVVGFFPANSVdHDDIEVYTDENRSQVLKKLHHLR---QQTEKRRGQpSHSLADFVMPKE 1071 ********************873699*********88777777765...666666666689********** PP TIGR02082 1043 sGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldk 1113 +G Dy+ga++v+ag +++ a+++e+ +ddy++ilvk+ladrlaea+ae +he vRk +wgy ++e+l++ NCBI__GCF_001995255.1:WP_077243567.1 1072 AGGPDYIGAFAVSAGGDVDAKAEEYEKANDDYHAILVKSLADRLAEAFAECMHEYVRKYYWGYVADEQLEN 1142 *********************************************************************** PP TIGR02082 1114 edllkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfa 1181 edl+ e+Y+Girpa+GYpacP+htekatl+eLl+ae+ ++ltes+a+ P ++vsg+yfahpe++Yf NCBI__GCF_001995255.1:WP_077243567.1 1143 EDLIEEKYQGIRPAPGYPACPEHTEKATLWELLQAEEnADMTLTESYAMLPVSAVSGWYFAHPESRYFG 1211 ***********************************999******************************5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1263 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 27.64 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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