Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_013450377.1 CALNI_RS01215 methionine synthase
Query= metacyc::G18NG-11090-MONOMER (1221 letters) >NCBI__GCF_000183405.1:WP_013450377.1 Length = 1126 Score = 874 bits (2258), Expect = 0.0 Identities = 502/1209 (41%), Positives = 720/1209 (59%), Gaps = 89/1209 (7%) Query: 17 EFLDALANHVLIGDGAMGTQLQGFDLDVEKDFLDLEGCNEILNDTRPDVLRQIHRAYFEA 76 +F+ + V++ DGAMGT +Q + + + + GCNE LN P ++ +IH + EA Sbjct: 3 DFVKFAKDRVILFDGAMGTNIQKYSIS-DATWQGKNGCNEYLNIVAPHIIEEIHGNFLEA 61 Query: 77 GADLVETNTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLG 136 GAD++ETN+FG L++Y + D E+ + +AR VAD+ G RFV GS+G Sbjct: 62 GADVLETNSFGGTRLVLSEYGLEDAVYEINLQAARIARRVADKYG-------RFVAGSVG 114 Query: 137 PGTKLPSLGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAEL 196 PGTKL SLGH Y DL YKE +L +IDGG D F+IET QD+LQ+KAA++G++ M E Sbjct: 115 PGTKLVSLGHISYDDLFYMYKEQSLALIDGGVDLFIIETCQDMLQIKAAINGIRSGMEEK 174 Query: 197 DTFLPIICHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKH 256 LPI+ VTVE GTML GS++ A + I +G+NCA GPD M E L LS Sbjct: 175 KVNLPIMVSVTVEINGTMLTGSDLSAVAVTMAGYPIYSLGINCALGPDLMYEPLTTLSNS 234 Query: 257 ADIPVSVMPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAV 316 +S +PNAGLP+ Y +E + +A+ + ++ + +S+VGGCCGT+ EHIR + Sbjct: 235 WGGRISCIPNAGLPMNINGKFVYNMEPDRMAEIIDDILNHFPISIVGGCCGTSYEHIREM 294 Query: 317 RDAVVGVPEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNS 376 R + K+P PV + + AS+YT+ L+QE ++IGER N+ Sbjct: 295 R---------KVCDKHKVP-DPV-----RFQVKGMAASIYTATSLNQEPPPALIGERANA 339 Query: 377 NGSKAFREAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSST 436 NGSKAFRE ++ D++ + I K Q + AH +D+CV Y GRD DMA +++ S Sbjct: 340 NGSKAFRELLIKEDFDGMLKIVKDQEEEAAHFVDICVAYAGRDEKRDMARFISMVNRMSL 399 Query: 437 LPIMIDSTEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTI 496 LP +ID+TEP+V+ L+ G+ I+NS+NFEDG + R++ LVK AAV+ LTI Sbjct: 400 LPAVIDTTEPDVLEEALKRYSGKPIINSINFEDGG---KKLHRVLNLVKDFPAAVIGLTI 456 Query: 497 DEEGQARTAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEA 556 DE+G A TA K IAKR+ T Y LD +D+++D LTF I +G E R ++T+EA Sbjct: 457 DEDGMAMTAAKKFEIAKRIYTVFTEEYHLDPEDLIIDPLTFSIGSGDETLRYAALQTLEA 516 Query: 557 IRELKKLYPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNR 616 I+ +K P + T LGLSN+SFGL+P +R +LNSVFL + +E+GLD AI H+SKILP Sbjct: 517 IKMIKNELPGVKTVLGLSNVSFGLSPKSRIILNSVFLKKAVESGLDMAIVHASKILPEAS 576 Query: 617 IDDRQREVALDMVYDRRTEDYDPLQEFMQLFEGVS----AADAKDARAEQLAAMPLFERL 672 I + ++AL+++ + L++F+ + + D D E+L L Sbjct: 577 IPTEEYDLALNLI----NGEEGALEKFINFYSAKKDDDISVDKNDISDEEL--------L 624 Query: 673 AQRIIDGDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAET 732 ++ GDK +E L+ +K +P IIN L++GM+ +GELFG G+M LPFVLQSAE Sbjct: 625 IVKLKKGDKTDIETLLDRLLKRYTPYDIINNILMSGMQEIGELFGKGKMLLPFVLQSAEV 684 Query: 733 MKTAVAYLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVN 792 MK +V+YLE FME+ E KGKIV+ATVKGDVHDIGKNLVDIILSNNGY V N Sbjct: 685 MKKSVSYLEKFMEK-------TDTEPKGKIVLATVKGDVHDIGKNLVDIILSNNGYRVYN 737 Query: 793 LGIKQPLSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALT 852 LGIK P+ M+E A E AD IGMSGLLVKST++MKEN+EE+ G V+LGGAALT Sbjct: 738 LGIKVPVEEMIEKAIEVGADAIGMSGLLVKSTIIMKENIEEIKRRGL-KVKVLLGGAALT 796 Query: 853 RTYVENDLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLDPNSPEAIEQAKKKAERKA 912 YV+N+ VY GEVYY +DAF+ + + E +K E Sbjct: 797 EGYVKNECAPVYDGEVYYCKDAFDAITYLQE---------------------EKGVESDV 835 Query: 913 RNERSRKIAAERKANAAPVIVPERSDVSTDTPTAAPPFWGTRIVKGLPLAEFLGNLDERA 972 +N+ KI ++ ++ V ++D+S+ T PPF G R+V+ + + L++R Sbjct: 836 QNDVDVKIDSKNDKDSLKPSV--KNDLSS-TIVPQPPFLGVRVVECINFDDVEKFLNKRT 892 Query: 973 LFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYFPAVAEG 1032 L+ +WG K + YE L+E +P L+++K ++D + L+YGYF V+ G Sbjct: 893 LWTNRWGYKKLKEQSNTEYEKLLEEVVKPEYNSILEKVKLSKLVD-MKLIYGYFRVVSVG 951 Query: 1033 DDVVILESPDPHAAERMRFSFPRQQRGRFLCIADFIRPREQAVKDGQVDVMPFQLVTMGN 1092 DDV+IL D E R +FPRQ+ +LC+AD+ +P ++ G VD++P Q+VT+G+ Sbjct: 952 DDVIIL---DERENEVERLTFPRQRVEPYLCLADYFKPLDK----GIVDILPLQIVTLGD 1004 Query: 1093 PIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELKLNDGGSVADFDPEDK 1152 +F +L +N Y+EY HG + TEA+AEYWH +R EL + + +P+ Sbjct: 1005 RPVEFLKKLKDSN-YKEYFLYHGFFTEFTEAVAEYWHRHIRYEL------GITENEPQSV 1057 Query: 1153 TKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEELQLHPEQSTDAFVLY 1212 YRG R+SFGY SCPDLE K++ELL+ +IGV ++E Q+ PE +T A +++ Sbjct: 1058 EGILTNRYRGLRYSFGYPSCPDLEGNKKIIELLDASKIGVSITETFQMVPEFTTSAIIVH 1117 Query: 1213 HPEAKYFNV 1221 +AKYF V Sbjct: 1118 SDKAKYFVV 1126 Lambda K H 0.316 0.135 0.386 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: 3045 Number of extensions: 130 Number of successful extensions: 15 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: 1221 Length of database: 1126 Length adjustment: 47 Effective length of query: 1174 Effective length of database: 1079 Effective search space: 1266746 Effective search space used: 1266746 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: 58 (26.9 bits)
Align candidate WP_013450377.1 CALNI_RS01215 (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.942328.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 1131.5 0.4 0 1131.1 0.4 1.1 1 NCBI__GCF_000183405.1:WP_013450377.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000183405.1:WP_013450377.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1131.1 0.4 0 0 2 1182 .] 9 1126 .] 8 1126 .] 0.95 Alignments for each domain: == domain 1 score: 1131.1 bits; conditional E-value: 0 TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntF 72 + r++++DGamGt++q++ + +a ++g+ +G+n++Ln+ P +i++ih +++eaGaD++etn F NCBI__GCF_000183405.1:WP_013450377.1 9 KDRVILFDGAMGTNIQKYSISDATWQGK--------NGCNEYLNIVAPHIIEEIHGNFLEAGADVLETNSF 71 679************************5........9********************************** PP TIGR02082 73 nsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvty 143 ++t ++l++Y+led +ye+n +aa++ar+vad+++ RfvaGs+GP++kl +l+ ++ y NCBI__GCF_000183405.1:WP_013450377.1 72 GGTRLVLSEYGLEDAVYEINLQAARIARRVADKYG------RFVAGSVGPGTKLVSLG---------HISY 127 ***********************************......*****************.........**** PP TIGR02082 144 delvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqt 214 d+l Ykeq +l+dGGvDl++iet++D+l++kaa++++++ +eek+++lPi++s v+v+ G++L+G++ NCBI__GCF_000183405.1:WP_013450377.1 128 DDLFYMYKEQSLALIDGGVDLFIIETCQDMLQIKAAINGIRSGMEEKKVNLPIMVS-VTVEINGTMLTGSD 197 ********************************************************.************** PP TIGR02082 215 leaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg...eYdltpeelakal 282 l a+++++ ++i +lG+nCalG+d++ e + +ls+ +s+iPnaGLP ++ Y+ +p+++a+++ NCBI__GCF_000183405.1:WP_013450377.1 198 LSAVAVTMAGYPIYSLGINCALGPDLMYEPLTTLSNSWGGRISCIPNAGLPMNINgkfVYNMEPDRMAEII 268 ***************************************************99987989************ PP TIGR02082 283 kefaeegllnivGGCCGttPehiraiaeavkdikprkrqele.eksvlsglealkiaqessfvniGeRtnv 352 + +++ ++ivGGCCGt ehir++ ++ ++ k ++ +++ + +++s+++a +++qe iGeR n+ NCBI__GCF_000183405.1:WP_013450377.1 269 DDILNHFPISIVGGCCGTSYEHIREMRKVCDKHKVPDPVRFQvKGMAASIYTATSLNQEPPPALIGERANA 339 ******************************999988887765156899*********************** PP TIGR02082 353 aGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDss 423 +Gsk fr+l+++ed++ +lki k+q ee a+ +Di+v ++++D ++dm +++s++ + +P ++D + NCBI__GCF_000183405.1:WP_013450377.1 340 NGSKAFRELLIKEDFDGMLKIVKDQEEEAAHFVDICVAYAGRDEKRDMARFISMVNRM---SLLPAVIDTT 407 ****************************************************987665...89******** PP TIGR02082 424 efevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykl 494 e +vle Lk+ Gk i+nsi+++dG ++ + ++l+k++ aav+ +++De+G+a ta+kk+eiakR+y++ NCBI__GCF_000183405.1:WP_013450377.1 408 EPDVLEEALKRYSGKPIINSINFEDGGKKLHRVLNLVKDFPAAVIGLTIDEDGMAMTAAKKFEIAKRIYTV 478 *********************************************************************** PP TIGR02082 495 ltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRea 565 te++ ++ped+i+Dp++++i+ G e + a++++eai+ ik+elP +k+ +G+snvsF+l ++ R + NCBI__GCF_000183405.1:WP_013450377.1 479 FTEEYHLDPEDLIIDPLTFSIGSGDETLRYAALQTLEAIKMIKNELPGVKTVLGLSNVSFGLS--PKSRII 547 ***************************************************************..****** PP TIGR02082 566 lhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskea 636 l+svFL +a+++GlDm+iv+a+k+++ + i+ e +++++li L ++++ y +k + + NCBI__GCF_000183405.1:WP_013450377.1 548 LNSVFLKKAVESGLDMAIVHASKILPEASIPTEEYDLALNLINGE----EGALEKFINFYSAKKDD-D--- 610 *****************************************9543....34577777777777766.3... PP TIGR02082 637 qeaewrnlpveeRLeralvkGeregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvk 707 + +++ ee L +l kG + ie l+ + k ++p +ii++ L+ Gm+ +G+LFG+Gkm LP+v++ NCBI__GCF_000183405.1:WP_013450377.1 611 ISVDKNDISDEELLIVKLKKGDKTDIETLLDRLL-KRYTPYDIINNILMSGMQEIGELFGKGKMLLPFVLQ 680 3455667888999*******************99.7889******************************** PP TIGR02082 708 sarvmkkavayLePylekekeedkskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekile 778 sa+vmkk+v+yLe ++ek + ++ kGkivlatvkGDvhDiGkn+vd++Ls+ngy+v +lG+kvPve+++e NCBI__GCF_000183405.1:WP_013450377.1 681 SAEVMKKSVSYLEKFMEKTD--TEPKGKIVLATVKGDVHDIGKNLVDIILSNNGYRVYNLGIKVPVEEMIE 749 *****************988..7899********************************************* PP TIGR02082 779 aakkkkaDviglsGLivksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdase 849 +a + aD ig+sGL+vks+ m+e++ee++rrg+k+ +llGGaal++ +v++++a+ Y+gev y kda++ NCBI__GCF_000183405.1:WP_013450377.1 750 KAIEVGADAIGMSGLLVKSTIIMKENIEEIKRRGLKVKVLLGGAALTEGYVKNECAPVYDGEVYYCKDAFD 820 *********************************************************************** PP TIGR02082 850 avkvvdkllsekkkaeelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtk 920 a++ + +e+k +e ++++ +++ + ++ k+ k++++ d+s + vp+p+flG++ NCBI__GCF_000183405.1:WP_013450377.1 821 AITYL----QEEK---GVESDVQNDVDVKIDSKN---------DKDSLKPSVKNDLS-STIVPQPPFLGVR 874 *9864....4443...234445555555555554.........33444566677888.7889********* PP TIGR02082 921 vleas.ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGl 989 v+e + +++ k++++++l++ W+ ++ ++ +++ e+e+l+++ + ++ +++l+k++ kl+ + ++G+ NCBI__GCF_000183405.1:WP_013450377.1 875 VVECInFDDVEKFLNKRTLWTnRWGYKKLKE-QSNTEYEKLLEEVVKPEYNSILEKVKLSKLVDMKLIYGY 944 *****9***************99****9999.99************************************* PP TIGR02082 990 fPaqsvgddieiytdetvsqetkpiatvrekleqlrqqsdrylclaDfiaskesGikDylgallvtaglga 1060 f svgdd+ i++++ v e+l ++rq + ylclaD++++ + Gi+D l++++vt g NCBI__GCF_000183405.1:WP_013450377.1 945 FRVVSVGDDVIILDEREN--------EV-ERLTFPRQRVEPYLCLADYFKPLDKGIVDILPLQIVTLGDRP 1006 *************95443........33.57899************************************* PP TIGR02082 1061 eelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131 e+ kkl++ ++++++ l ++ ++ea+ae++h+++R el + e+e++++e +l +rYrG r++fGYp NCBI__GCF_000183405.1:WP_013450377.1 1007 VEFLKKLKD-SNYKEYFLYHGFFTEFTEAVAEYWHRHIRYELGIT-ENEPQSVEGILTNRYRGLRYSFGYP 1075 *******86.589*****************************988.************************* PP TIGR02082 1132 acPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182 +cPd++ +++++eLl+a +iG+ +te +++ Pe ++s+++++ +akYf v NCBI__GCF_000183405.1:WP_013450377.1 1076 SCPDLEGNKKIIELLDASKIGVSITETFQMVPEFTTSAIIVHSDKAKYFVV 1126 *************************************************76 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1182 nodes) Target sequences: 1 (1126 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 0.03s 00:00:00.07 Elapsed: 00:00:00.07 # Mc/sec: 18.80 // [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