Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 349708 BT0180 5-methyltetrahydrofolate-homocysteine methyltransferase (NCBI ptt file)
Query= CharProtDB::CH_090726 (1227 letters) >FitnessBrowser__Btheta:349708 Length = 915 Score = 1049 bits (2713), Expect = 0.0 Identities = 522/904 (57%), Positives = 680/904 (75%), Gaps = 5/904 (0%) Query: 12 LNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAY 71 ++ERIL+LDG MGTMIQ Y L E DFRGERFA P LKGNNDLL L++P+VI IH Y Sbjct: 9 VSERILILDGAMGTMIQQYNLKEEDFRGERFAHIPGQLKGNNDLLCLTRPDVIQDIHRKY 68 Query: 72 FEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAG 131 EAGADIIETNTF+STT++MADY +E EIN AA +LAR ADE+TA++P+KPR+VAG Sbjct: 69 LEAGADIIETNTFSSTTVSMADYHVEEYVREINLAATRLARELADEYTAKSPDKPRFVAG 128 Query: 132 VLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKA 191 +GPTN+T S+SPDVN+PAFR +++D L A+Y++ +A++EGG D ILIET+FDTLNAKA Sbjct: 129 SVGPTNKTCSMSPDVNNPAFRALSYDELAASYQQQMEAMLEGGVDAILIETIFDTLNAKA 188 Query: 192 AVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGP 251 A+FA + G+E+P+M+S T++D GRTLSGQT EAF S++HA + GLNC+ G Sbjct: 189 AIFAAGQAMKVTGIEVPVMLSVTVSDIGGRTLSGQTLEAFLASVQHANIFSVGLNCSFGA 248 Query: 252 DELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCC 311 +L+ ++++L+ A Y++A+PNAGLPN+ G+YD MA +++E+ Q G +NI+GGCC Sbjct: 249 RQLKPFLEQLASRAPYYISAYPNAGLPNSLGKYDQTPADMAHEVKEYIQEGLVNIIGGCC 308 Query: 312 GTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKF 371 GTT +IA + G P P LSGLE L + + FVN+GER NV GS KF Sbjct: 309 GTTDAYIAEYQTLIAGAKPHVPAPKPDCMWLSGLELLEVKPEINFVNIGERCNVAGSRKF 368 Query: 372 KRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPI 431 RL+ E+KY EAL +ARQQVE+GA +ID+NMD+G+LDA M FLNLI EP+IARVP+ Sbjct: 369 LRLVNEKKYDEALSIARQQVEDGALVIDVNMDDGLLDARTEMTTFLNLIMSEPEIARVPV 428 Query: 432 MIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQA 491 MIDSSKW+VIE GLKC+QGK IVNSIS+KEG + F+ HA+++++YGAA VVMAFDE+GQA Sbjct: 429 MIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLEHARIIKQYGAATVVMAFDEKGQA 488 Query: 492 DTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKR 551 DT ARKIE+C RAY++L ++VGF P DIIFDPN+ AVATGIEEHNNYA DFI A I++ Sbjct: 489 DTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIEATGWIRK 548 Query: 552 ELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAE 611 LP A +SGGVSN+SFSFRGN+ +REA+HAVFLY+AI+ GMDMGIVN G +Y D+PA+ Sbjct: 549 NLPGAHVSGGVSNLSFSFRGNNYIREAMHAVFLYHAIQQGMDMGIVNPGTSVLYSDIPAD 608 Query: 612 LRDAVEDVILNRRDDGTERLLELAEKYRGSK--TDDTANAQQAEWRSWEVNKRLEYSLVK 669 + +EDV+LNRR D ERL+ELAE + + T A +Q WR V +RL+Y+L+K Sbjct: 609 TLEKIEDVVLNRRPDAAERLIELAEALKETMGGTSGQAAVKQDAWREESVQERLKYALMK 668 Query: 670 GITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAV 729 GI +++EQD EA + ++VIEGPLMDGMN VG+LFG GKMFLPQVVK+AR MK+AV Sbjct: 669 GIGDYLEQDLAEALPLYDKAVDVIEGPLMDGMNYVGELFGAGKMFLPQVVKTARTMKKAV 728 Query: 730 AYLEPFIEASKEQGKTN-GKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEK 788 A L+P IE+ K +G ++ GK+++ATVKGDVHDIGKNIV VV+ CN Y+IVDLGVMVPAE Sbjct: 729 AILQPIIESEKVEGSSSAGKVLLATVKGDVHDIGKNIVAVVMACNGYDIVDLGVMVPAET 788 Query: 789 ILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQ 848 I++ A E D+IGLSGLITPSL+EM +VA E+E+ G IPLLIGGATTSK HTA+KI Sbjct: 789 IVQRAIEEKVDMIGLSGLITPSLEEMTHVAAELEKAGLDIPLLIGGATTSKMHTALKIAP 848 Query: 849 NYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLEA 908 Y P V++++AS+ V + LL+ + + + EY+ +R + G + T V+LE Sbjct: 849 VYHAPVVHLKDASQNASVASRLLNSQMKAELINELDAEYQALREKSGLLRRET--VSLEE 906 Query: 909 ARDN 912 A+ N Sbjct: 907 AQKN 910 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: 2561 Number of extensions: 104 Number of successful extensions: 3 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: 915 Length adjustment: 45 Effective length of query: 1182 Effective length of database: 870 Effective search space: 1028340 Effective search space used: 1028340 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: 58 (26.9 bits)
Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate 349777 BT0249 5-methyltetrahydrofolate--homocysteine methyltransferase or methionine synthase (NCBI ptt file)
Query= CharProtDB::CH_090726 (1227 letters) >FitnessBrowser__Btheta:349777 Length = 300 Score = 195 bits (495), Expect = 5e-54 Identities = 125/304 (41%), Positives = 169/304 (55%), Gaps = 30/304 (9%) Query: 938 IETLRNYIDWTPFFMTWSLAGKYPRIL------------------EDEVVGVEAQRLFKD 979 I + YI+W FF W ++ I ED EA +LFK+ Sbjct: 7 IHNVAPYINWIYFFHAWGFQPRFAAIANIHGCDVCRASWLTTFPEEDRNKASEAMQLFKE 66 Query: 980 ANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSHHLRQQTEKT-GF 1038 AN MLD L +K R + L AN GD++ I E T V LRQQT K G Sbjct: 67 ANRMLDLL--DKDYEVRTIFKLCKANSDGDNLVI---EKETDQFLVFPLLRQQTPKRDGS 121 Query: 1039 ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNKIMVKALADRLAEA 1098 +CL+DF+ P SG D IGAFA + + L + D Y ++V+ L+DRLAEA Sbjct: 122 PFFCLSDFIRPLSSGIPDTIGAFASCIDADMEGLYE-----QDPYKHLLVQTLSDRLAEA 176 Query: 1099 FAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEHTEKATIWELLEVE 1158 E +HE VRK WGYA +E LS +L+ E YQGIRPA GYP+ P+ + + ELL++ Sbjct: 177 ATEKMHEYVRKEAWGYAKDEILSMPDLLVEKYQGIRPAVGYPSLPDQSINFLLDELLDM- 235 Query: 1159 KHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYARRKGMSVTEVERWL 1218 K G+ LTE+ AM+P ASV G F+HP ++Y++V +I DQ+EDYARR+G S E+ ++L Sbjct: 236 KQIGITLTENGAMYPHASVCGLMFAHPAAEYFSVGKIGEDQLEDYARRRGKSTEEMRKFL 295 Query: 1219 APNL 1222 A NL Sbjct: 296 AANL 299 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: 760 Number of extensions: 30 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: 300 Length adjustment: 37 Effective length of query: 1190 Effective length of database: 263 Effective search space: 312970 Effective search space used: 312970 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: 53 (25.0 bits)
Align candidate 349708 BT0180 (5-methyltetrahydrofolate-homocysteine methyltransferase (NCBI ptt file))
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.15593.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 1339.5 5.2 0 1339.2 5.2 1.0 1 lcl|FitnessBrowser__Btheta:349708 BT0180 5-methyltetrahydrofolate- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:349708 BT0180 5-methyltetrahydrofolate-homocysteine methyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1339.2 5.2 0 0 2 900 .. 10 911 .. 9 914 .. 0.98 Alignments for each domain: == domain 1 score: 1339.2 bits; conditional E-value: 0 TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFnste 76 ++ril+lDGamGt++q++nL+e+dFrge +a+++ +lkGnndlL lt+P+vi++ihr+y+eaGaDi+etntF+st+ lcl|FitnessBrowser__Btheta:349708 10 SERILILDGAMGTMIQQYNLKEEDFRGErFAHIPGQLKGNNDLLCLTRPDVIQDIHRKYLEAGADIIETNTFSSTT 85 68************************************************************************** PP TIGR02082 77 ialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtydelvdaYk 151 +++adY++e+ ++e+n +a++lare ade+t ++p+k+RfvaGs+GPtnk+ ++spdv++p+fr + ydel ++Y+ lcl|FitnessBrowser__Btheta:349708 86 VSMADYHVEEYVREINLAATRLARELADEYTaKSPDKPRFVAGSVGPTNKTCSMSPDVNNPAFRALSYDELAASYQ 161 **************************************************************************** PP TIGR02082 152 eqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtleaflaslehaei 227 +q++++l+GGvD++Liet+fDtlnakaa+fa+ ++++ g+e+P+++s ++ d GrtLsGqtleaflas++ha+i lcl|FitnessBrowser__Btheta:349708 162 QQMEAMLEGGVDAILIETIFDTLNAKAAIFAAGQAMKVTGIEVPVMLSVTVSDIGGRTLSGQTLEAFLASVQHANI 237 **************************************************************************** PP TIGR02082 228 lilGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPe 303 +++GLnC++Ga +l++f+++l+ a+ ++s++PnaGLPn+lg+Yd+tp +a+++ke+++egl+ni+GGCCGtt + lcl|FitnessBrowser__Btheta:349708 238 FSVGLNCSFGARQLKPFLEQLASRAPYYISAYPNAGLPNSLGKYDQTPADMAHEVKEYIQEGLVNIIGGCCGTTDA 313 **************************************************************************** PP TIGR02082 304 hiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqve 379 +i++ + +++ kp+ ++ + lsgle l++++e +fvniGeR+nvaGs+kf +l+++++y+eal+ia+qqve lcl|FitnessBrowser__Btheta:349708 314 YIAEYQTLIAGAKPHVPAPKPDCMWLSGLELLEVKPEINFVNIGERCNVAGSRKFLRLVNEKKYDEALSIARQQVE 389 **************************************************************************** PP TIGR02082 380 eGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFle 455 +Ga ++D+n+D++llD++++m+++l+l+ sep+ia+vP+m+Dss++ev+eaGLk++qGk+ivnsislk+Gee Fle lcl|FitnessBrowser__Btheta:349708 390 DGALVIDVNMDDGLLDARTEMTTFLNLIMSEPEIARVPVMIDSSKWEVIEAGLKCLQGKSIVNSISLKEGEEVFLE 465 **************************************************************************** PP TIGR02082 456 kaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfie 531 +a++ik+yGaa vvmafDe+Gqa+ta++kie+++Ray+ll++kvgf+p+diifDpn+l++atGieeh++ya+dfie lcl|FitnessBrowser__Btheta:349708 466 HARIIKQYGAATVVMAFDEKGQADTAARKIEVCERAYRLLVDKVGFNPHDIIFDPNVLAVATGIEEHNNYAVDFIE 541 **************************************************************************** PP TIGR02082 532 aireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedli 607 a+ +i+++lP a++sgGvsn+sFs+rgn+ +Rea+h+vFLy+ai++G+Dmgivn+g +y di+++ +e++ed++ lcl|FitnessBrowser__Btheta:349708 542 ATGWIRKNLPGAHVSGGVSNLSFSFRGNNYIREAMHAVFLYHAIQQGMDMGIVNPGTSVLYSDIPADTLEKIEDVV 617 **************************************************************************** PP TIGR02082 608 ldrrreatekLlelaelykgtkeks..skeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleiie 681 l+rr++a e+L elae k+t + ++ ++++wr+ +v+eRL++al+kG+ +++e+dl ea+ + +++++ie lcl|FitnessBrowser__Btheta:349708 618 LNRRPDAAERLIELAEALKETMGGTsgQAAVKQDAWREESVQERLKYALMKGIGDYLEQDLAEALPLYDKAVDVIE 693 ******************998654411567799******************************************* PP TIGR02082 682 gpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivlatvkGDvhDiGknivdvv 756 gpL+dGm+ vG+LFG+GkmfLPqvvk ar+mkkava L+P +e ek e +s+Gk++latvkGDvhDiGkniv vv lcl|FitnessBrowser__Btheta:349708 694 GPLMDGMNYVGELFGAGKMFLPQVVKTARTMKKAVAILQPIIESEKVEGsSSAGKVLLATVKGDVHDIGKNIVAVV 769 **********************************************8864889*********************** PP TIGR02082 757 LscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavk 832 ++cngy++vdlGv+vP+e+i++ a ++k D+iglsGLi++sl+em++va e+e+ g++iPll+GGa++sk h+a k lcl|FitnessBrowser__Btheta:349708 770 MACNGYDIVDLGVMVPAETIVQRAIEEKVDMIGLSGLITPSLEEMTHVAAELEKAGLDIPLLIGGATTSKMHTALK 845 **************************************************************************** PP TIGR02082 833 iaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkev 900 ia+ Y+++vv+ kdas++ +v+++ll+ + kae ++++ +ey+ +rek g +++++s+++a+k++ lcl|FitnessBrowser__Btheta:349708 846 IAPVYHAPVVHLKDASQNASVASRLLNSQMKAELINELDAEYQALREKSGL--LRRETVSLEEAQKNK 911 ************************************************999..566667777777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (915 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: 0.09u 0.04s 00:00:00.13 Elapsed: 00:00:00.12 # Mc/sec: 8.75 // [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