Align Methionine synthase; EC 2.1.1.13; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12 dependent; MS (uncharacterized)
to candidate WP_078430828.1 BK574_RS10060 methionine synthase
Query= curated2:Q5E814 (1226 letters) >NCBI__GCF_002019605.1:WP_078430828.1 Length = 1148 Score = 810 bits (2093), Expect = 0.0 Identities = 471/1194 (39%), Positives = 724/1194 (60%), Gaps = 57/1194 (4%) Query: 7 KVQIEKQLSERILLIDGGMGTMIQGYKFEEEDYRGERFNKWHCDLKGNNDLLVLSQPQII 66 K + E+QL ++IL++DG MGTM+Q ED+ GE + +G N+ L ++ P +I Sbjct: 3 KNKFEQQLEKKILVLDGAMGTMLQDANLTAEDFGGEEY-------EGCNEYLNITAPHVI 55 Query: 67 RDIHEAYLEAGADILETNTFNATTIAMADYDMESLSEEINFEAAKLAREVADKWTEKTPN 126 IH AY EAGADI+ETNTF AT I + DYD++ L+EE+N +AA++A++VA++++ T Sbjct: 56 EYIHRAYFEAGADIVETNTFGATDIVLEDYDLQHLAEELNIKAAQIAKKVAEEFS--TSE 113 Query: 127 KPRYVAGVLGPTNRTCSISPDVNDPGFRNVSFDELVEAYSESTRALIRGGSDLILIETIF 186 PR+VAG +GPT ++ S++ V+FD+L++AY + LI+GG D++L+ET Sbjct: 114 HPRFVAGAMGPTTKSLSVTG--------GVTFDQLIKAYEQQVIGLIKGGVDVLLLETSQ 165 Query: 187 DTLNAKACSFAVESVFEELDITLPVMISGTITDASGRTLSGQTTEAFYNALRHVKPISFG 246 DT N KA +E F++L++ +P+++SGTI + G TL+GQ EAFY ++ H+ P G Sbjct: 166 DTRNVKAAYLGIERAFKQLNVKMPILVSGTI-EPMGTTLAGQNIEAFYLSIEHMTPTVVG 224 Query: 247 LNCALGPDELREYVSDLSRISECYVSAHPNAGLPNAFGEYDLSPEDMAEHVAEWASSGFL 306 LNCA GP+ +++++ LS ++ YVS +PNAGLP+ G+Y +PE + + + +A G+L Sbjct: 225 LNCATGPEFMQDHIRSLSDLATSYVSCYPNAGLPDEDGKYHETPESLTKKLTAFAEKGWL 284 Query: 307 NLIGGCCGTTPEHIRQMALVVEGVKPRQLPE-LPVACRLSGLEPLTIEKDSLFINVGERT 365 NL+GGCCGTTP HI+ M+ ++ +PR+L E P A +SG+EPL ++ + VGERT Sbjct: 285 NLVGGCCGTTPAHIKAMSEAMKSYQPRKLNEGHPHA--VSGIEPLVYDESMRPLFVGERT 342 Query: 366 NVTGSARFKRLIKEELYDEALSVAQEQVENGAQIIDINMDEGMLDAEACMVRFLNLCASE 425 NV GS +FK LI + LY+EA +A+ QV+ GA IIDI + + + + M FL ++ Sbjct: 343 NVIGSRKFKNLIADGLYEEASEIARSQVKKGAHIIDICLADPDREEKEDMEHFLKYVVNK 402 Query: 426 PEISKVPVMVDSSKWEVIEAGLKCIQGKGIVNSISLKEGKEKFVHQAKLIRRYGAAVIVM 485 KVP+M+DS+ EV+E L QGK I+NSI+L++G+E+F L+ RYGAAV+V Sbjct: 403 V---KVPLMIDSTDEEVLELALTYSQGKAIINSINLEDGEERFEKVIPLVHRYGAAVVVG 459 Query: 486 AFDEVGQADTRERKIEICTNAYNILVDEVGFPPEDIIFDPNIFAVATGIDEHNNYAVDFI 545 DE G A T +RK+E+ +Y++LV++ G P DIIFDP +F V TG +++ A + + Sbjct: 460 TIDEEGMAVTAKRKLEVAKRSYDLLVNKYGLQPSDIIFDPLVFPVGTGDEQYIGSAKETV 519 Query: 546 EAVGDIKRTLPHAMISGGVSNVSFSFRGNNYVREAIHAVFLYHCFKNGMDMGIVNAGQLE 605 E + IK LP + GVSNVSF RE ++AV+LYHC + G+D IVN +LE Sbjct: 520 EGIRLIKEALPECLTILGVSNVSFGL--PQVGREVLNAVYLYHCTQAGLDYAIVNTEKLE 577 Query: 606 IYDNVPEDLREAVEDVVLNRRDDSTERLLDIATEYLERAVGKVEDKSALEWRDWPVEKRL 665 Y ++PE+ ++ + ++ + D E L + Y V KVE K ++ + +E+RL Sbjct: 578 RYASIPENEKQLSDKLLFDTND---ETLAEFTAFY---RVKKVEKK--VQTSNLSLEERL 629 Query: 666 EHSLVKGITEFIVEDTEEARINAEKPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSAR 725 +V+G E ++ED ++A +P+++I GPLM+GM+ VG LF ++ + +V++SA Sbjct: 630 ASYIVEGTKEGLIEDLKQALEKYTEPLDIINGPLMNGMDEVGRLFNNNELIVAEVLQSAE 689 Query: 726 VMKQAVAHLEPFINASKEVGATNGKILLATVKGDVHDIGKNIVGVVLQCNNYEIIDLGVM 785 VMK +VA LE ++ K GKILLATVKGDVHDIGKN+V ++L N ++I++LG+ Sbjct: 690 VMKASVAFLEQYME-KKSGDNGKGKILLATVKGDVHDIGKNLVEIILGNNGFKIVNLGIK 748 Query: 786 VSCETILKVAKEENVDIIGLSGLITPSLDEMVHVAKEMERQGFDLPLLIGGATTSKAHTA 845 V+ +++ K EN D IGLSGL+ S +MV A++++ Q +P+L+GGA ++ T Sbjct: 749 VTSNELIEAVKRENPDAIGLSGLLVKSAQQMVLTAQDLKEQNISIPILVGGAALTRKFTD 808 Query: 846 VKIEQNYSQPVVYVNNASRAVGVCTSLL-SDELKPSFVEKLDIDYERVREQHSRKQPRTK 904 +I + Y V+Y +A + + L+ DELK KL+ D + +Q ++ K Sbjct: 809 NRISREYDGVVLYAKDAMNGLDLANKLVKEDELK-----KLEEDKQTKLQQVGNEETEKK 863 Query: 905 -PVTLEVARANKVAIDWASYTPPVPLKPGVHIFDNFDVSTLRNYIDWTPFF-MTWSLVGK 962 VT E+ R+ + P L+P HI + +S L YI+ L GK Sbjct: 864 NKVTTELPRSKVSQV--VPIHKPNDLQP--HILKEYKISHLEPYINLQMLLGKHLGLHGK 919 Query: 963 YPKILDHEEVGEEAKRLFKDANDLLDRVEKEGLLKARGMCALFPASSVGDDIEVY-TDES 1021 ++L E E+A L + LL + GLL+ARGM FPA S G+DI +Y + Sbjct: 920 VSRLL--AEGDEKAHTLKDKVDSLLYEAKTNGLLQARGMYQFFPAQSKGNDIIIYDPQDE 977 Query: 1022 RTKVAKVLHNLRQQTEKPKGFNYCLSDYIAPKESGKNDWIGGFAVTGGIGERELADEYKA 1081 +T++ + + +Q +P CL+DY+ +SG+ D++G AVT GIG RE A + K Sbjct: 978 KTEIER--FSFPRQNHEP---FLCLADYVRSIDSGEMDYVGFLAVTAGIGVREKAMKAKD 1032 Query: 1082 NGDDYNAIMIQAVADRLAEAFAEYLHEKVRKEIWGYSPNETLSNDDLIREKYQGIRPAPG 1141 GD + +IQA A LAE FAE H+ +R + WG+ L+ D KYQG+R + G Sbjct: 1033 EGDYLFSHLIQATALELAEGFAERTHQLIRDQ-WGFPDPVELTMVDRFSAKYQGVRVSFG 1091 Query: 1142 YPACPEHTEKGALWELMNVEESIGMSLTSSYAMWPGASVSGMYFSHPDSRYFAI 1195 YPACP ++ L++L+ E IG+ LT + M P ASV+ M FSHP+ RYF + Sbjct: 1092 YPACPNLEDQAKLFKLLQ-PEKIGIKLTEEFMMEPEASVTAMVFSHPEGRYFNV 1144 Lambda K H 0.317 0.135 0.394 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: 3211 Number of extensions: 169 Number of successful extensions: 16 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: 1226 Length of database: 1148 Length adjustment: 47 Effective length of query: 1179 Effective length of database: 1101 Effective search space: 1298079 Effective search space used: 1298079 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 (21.6 bits) S2: 59 (27.3 bits)
Align candidate WP_078430828.1 BK574_RS10060 (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.15418.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 1295.1 3.9 0 1294.9 3.9 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078430828.1 BK574_RS10060 methionine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078430828.1 BK574_RS10060 methionine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1294.9 3.9 0 0 1 1182 [] 10 1144 .. 10 1144 .. 0.95 Alignments for each domain: == domain 1 score: 1294.9 bits; conditional E-value: 0 TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67 l+k+ilvlDGamGt+lq anLt++dF ge e++G+n++Ln+t P vi+ ihrayfeaGaDiv lcl|NCBI__GCF_002019605.1:WP_078430828.1 10 LEKKILVLDGAMGTMLQDANLTAEDFGGE------EYEGCNEYLNITAPHVIEYIHRAYFEAGADIV 70 579*************************7......9******************************* PP TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134 etntF++t i+l+dYdl+++a eln kaa++a++va+ef+ t+e++RfvaG++GPt+k +++ lcl|NCBI__GCF_002019605.1:WP_078430828.1 71 ETNTFGATDIVLEDYDLQHLAEELNIKAAQIAKKVAEEFS-TSEHPRFVAGAMGPTTKSLSVT---- 132 ****************************************.*******************999.... PP TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201 vt+d+l +aY++qv gl+ GGvD+lL+et +Dt n+kaa +++e++f++ ++++Pil+sg+ lcl|NCBI__GCF_002019605.1:WP_078430828.1 133 ----GGVTFDQLIKAYEQQVIGLIKGGVDVLLLETSQDTRNVKAAYLGIERAFKQLNVKMPILVSGT 195 ....789**********************************************************87 PP TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268 i + +G+tL Gq++eaf+ s+eh+ ++GLnCa+G++ ++++++ ls a+ +vs++PnaGLP++ lcl|NCBI__GCF_002019605.1:WP_078430828.1 196 I-EPMGTTLAGQNIEAFYLSIEHMTPTVVGLNCATGPEFMQDHIRSLSDLATSYVSCYPNAGLPDED 261 5.99*************************************************************** PP TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335 g+Y++tpe+l k+l+ fae+g ln+vGGCCGttP+hi+a++ea+k +prk +e +++ ++sg+e+l lcl|NCBI__GCF_002019605.1:WP_078430828.1 262 GKYHETPESLTKKLTAFAEKGWLNLVGGCCGTTPAHIKAMSEAMKSYQPRKLNEGHPH-AVSGIEPL 327 ***************************************************9987665.679***** PP TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402 +++ + +GeRtnv Gs+kf++li ++ yeea +ia++qv++Ga+i+Di++ + ++ ++dm++ lcl|NCBI__GCF_002019605.1:WP_078430828.1 328 VYDESMRPLFVGERTNVIGSRKFKNLIADGLYEEASEIARSQVKKGAHIIDICLADPDREEKEDMEH 394 ******************************************************************* PP TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469 +l+ ++++ + kvPlm+Ds++ evle L qGkai+nsi+l+dGeerF + + l+++yGaavvv lcl|NCBI__GCF_002019605.1:WP_078430828.1 395 FLKYVVNK--V-KVPLMIDSTDEEVLELALTYSQGKAIINSINLEDGEERFEKVIPLVHRYGAAVVV 458 ********..6.******************************************************* PP TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536 ++DeeG+a ta++k+e+akR y+ll++k+g++p+diifDp++++++tG e a++++e ir i lcl|NCBI__GCF_002019605.1:WP_078430828.1 459 GTIDEEGMAVTAKRKLEVAKRSYDLLVNKYGLQPSDIIFDPLVFPVGTGDEQYIGSAKETVEGIRLI 525 ******************************************************************* PP TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603 ke lP++ + +GvsnvsF+l + Re+l++v+Ly++ +aGlD +ivn+ kl+ y+ i+++ +++ lcl|NCBI__GCF_002019605.1:WP_078430828.1 526 KEALPECLTILGVSNVSFGLP--QVGREVLNAVYLYHCTQAGLDYAIVNTEKLERYASIPENEKQLS 590 ********************9..999***************************************** PP TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670 l++d ++ e L e++ y+ +k + ++ + nl++eeRL+ +v+G++eg+ edl++a+ lcl|NCBI__GCF_002019605.1:WP_078430828.1 591 DKLLFDTND---ETLAEFTAFYRVKKVE-----KKVQTSNLSLEERLASYIVEGTKEGLIEDLKQAL 649 *****9876...5688899888877777.....34567899************************** PP TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkiv 737 +k+++pl+ii+gpL++Gm+ vG LF + ++ + v++sa+vmk++va+Le y+ek+ d+ kGki+ lcl|NCBI__GCF_002019605.1:WP_078430828.1 650 EKYTEPLDIINGPLMNGMDEVGRLFNNNELIVAEVLQSAEVMKASVAFLEQYMEKKS-GDNGKGKIL 715 ******************************************************976.999****** PP TIGR02082 738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804 latvkGDvhDiGkn+v+++L++ng+++v+lG+kv ++++ea k++++D iglsGL+vks ++mv lcl|NCBI__GCF_002019605.1:WP_078430828.1 716 LATVKGDVHDIGKNLVEIILGNNGFKIVNLGIKVTSNELIEAVKRENPDAIGLSGLLVKSAQQMVLT 782 ******************************************************************* PP TIGR02082 805 aeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekik 871 a+++++++++iP+l+GGaal+++++++ i ++Y+g v+y+kda++++ +++kl++e++ ++ e + lcl|NCBI__GCF_002019605.1:WP_078430828.1 783 AQDLKEQNISIPILVGGAALTRKFTDNRISREYDGVVLYAKDAMNGLDLANKLVKEDELKKLEEDKQ 849 ******************************************************9997555434333 PP TIGR02082 872 eeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwka 937 + ++++ +e+ ek+++++++ r++v ++ + + +p++l ++l+++ i +l +yi++++ lcl|NCBI__GCF_002019605.1:WP_078430828.1 850 T---KLQQVGNEETEKKNKVTTELPRSKVSQV-----VPIHKPNDLQPHILKEYkISHLEPYINLQM 908 3...4444445555666777777777544443.....456789999999****************** PP TIGR02082 938 lFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiyt 1003 l + +l+gk + l + +++a+ l +++++ll + ++++ll+arg++ +fPaqs+g+di iy+ lcl|NCBI__GCF_002019605.1:WP_078430828.1 909 LLGkHLGLHGKVSRLLAEG--DEKAHTLKDKVDSLLYEAKTNGLLQARGMYQFFPAQSKGNDIIIYD 973 *99799*******888775..667899999************************************* PP TIGR02082 1004 detvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglgaeelakkleak 1070 ++ t +e++ ++rq+ + +lclaD+++s +sG+ Dy+g+l+vtag+g++e a k +++ lcl|NCBI__GCF_002019605.1:WP_078430828.1 974 PQ-------DEKTEIERFSFPRQNHEPFLCLADYVRSIDSGEMDYVGFLAVTAGIGVREKAMKAKDE 1033 44.......446778899************************************************* PP TIGR02082 1071 eddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdht 1137 d+ s l++a a lae +ae +h+ +R ++ + + +l + d + +Y+G+r +fGYpacP+++ lcl|NCBI__GCF_002019605.1:WP_078430828.1 1034 GDYLFSHLIQATALELAEGFAERTHQLIRDQWGFP-DPVELTMVDRFSAKYQGVRVSFGYPACPNLE 1099 *****************************987777.77778999*********************** PP TIGR02082 1138 ekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182 ++a+l++Ll++e+iG+klte+++++Peasv++++f+hpe +Yf+v lcl|NCBI__GCF_002019605.1:WP_078430828.1 1100 DQAKLFKLLQPEKIGIKLTEEFMMEPEASVTAMVFSHPEGRYFNV 1144 *******************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1148 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: 0.12u 0.04s 00:00:00.16 Elapsed: 00:00:00.15 # Mc/sec: 8.97 // [ok]
This GapMind analysis is from Apr 10 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