Align cobalamin-dependent methionine synthase (EC 2.1.1.13) (characterized)
to candidate WP_009543124.1 CCE_RS00370 methionine synthase
Query= metacyc::G18NG-11090-MONOMER
(1221 letters)
>NCBI__GCF_000017845.1:WP_009543124.1
Length = 1193
Score = 999 bits (2583), Expect = 0.0
Identities = 553/1223 (45%), Positives = 764/1223 (62%), Gaps = 74/1223 (6%)
Query: 26 VLIGDGAMGTQLQGFDLDVEKDF--LDLEGCNEILNDTRPDVLRQIHRAYFEAGADLVET 83
VL+ DGA GT LQ +L + DF + EGCNE L T+P+ + ++HR + E GAD++ET
Sbjct: 16 VLVFDGATGTSLQSQNLTAD-DFGGPEYEGCNEYLVHTKPEAVEKVHRGFLEVGADVIET 74
Query: 84 NTFGCNLPNLADYDIADRCRELAYKGTAVAREVADEMGPGRNGMRRFVVGSLGPGTKLPS 143
+TFG LA+YD+AD+ L K +A+++A E RFV GS+GPGTKLP+
Sbjct: 75 DTFGGTSIVLAEYDLADKAYYLNKKAAEIAKKMAAEYSTPEKP--RFVAGSMGPGTKLPT 132
Query: 144 LGHAPYADLRGHYKEAALGIIDGGGDAFLIETAQDLLQVKAAVHGVQDAMAELDTFLPII 203
LGH + LR Y E A G+ DGG D +IET QD+LQ+KAA++ V+ + LPI+
Sbjct: 133 LGHIDFDTLRDAYIEQAEGLYDGGADLLIIETCQDVLQIKAALNAVEAVFEKKRNRLPIM 192
Query: 204 CHVTVETTGTMLMGSEIGAALTALQPLGIDMIGLNCATGPDEMSEHLRYLSKHADIPVSV 263
+T+ET GTML+G+EI AAL L+P ID++GLNCATGP++M EH++YLS+H+ VS
Sbjct: 193 VSITMETMGTMLVGTEISAALAILEPYKIDILGLNCATGPEQMKEHIKYLSEHSPFIVSC 252
Query: 264 MPNAGLPVLGKNGAEYPLEAEDLAQALAGFVSEYGLSMVGGCCGTTPEHIRAVRDAVVGV 323
+PNAGLP A Y L +L AL F+ + G+ ++GGCCGT P+HI+A+ + +
Sbjct: 253 IPNAGLPENVGGQAHYRLTPIELKMALMHFIEDLGVQIIGGCCGTRPDHIKALSELSQDL 312
Query: 324 PEQETSTLTKIPAGPVEQASREVEKEDSVASLYTSVPLSQETGISMIGERTNSNGSKAFR 383
+E R + E S AS+Y++ P Q+ ++GER N++GSK R
Sbjct: 313 TPKE----------------RHPDYEPSAASIYSTQPYIQDNSFLIVGERLNASGSKKCR 356
Query: 384 EAMLSGDWEKCVDIAKQQTRDGAHMLDLCVDYVGRDGTADMATLAALLATSSTLPIMIDS 443
+ + + DW+ V +AK Q ++GAH+LD+ VDYVGRDG DM LA+ L + TLP+M+DS
Sbjct: 357 QLLDAEDWDSLVSLAKSQVKEGAHVLDVNVDYVGRDGVRDMHELASRLVNNITLPLMLDS 416
Query: 444 TEPEVIRTGLEHLGGRSIVNSVNFEDGDGPESRYQRIMKLVKQHGAAVVALTIDEEGQAR 503
TE + + +GL+ GG+ I+NS N+EDG E R+ ++++L K++GA VV TIDEEG R
Sbjct: 417 TEWQKMESGLKVAGGKCILNSTNYEDG---EERFLKVLELAKKYGAGVVVGTIDEEGMGR 473
Query: 504 TAEHKVRIAKRLIDDITGSYGLDIKDIVVDCLTFPISTGQEETRRDGIETIEAIRELKKL 563
TA+ K IAKR + YG+ +I D L PISTG EE R +G T+EAI+ +++
Sbjct: 474 TADKKFEIAKRAYNAAI-DYGIPAHEIFFDPLALPISTGIEEDRENGKATVEAIKRIREE 532
Query: 564 YPEIHTTLGLSNISFGLNPAARQVLNSVFLNECIEAGLDSAIAHSSKILPMNRIDDRQRE 623
P H LG+SNISFGLNPAARQVLNSVFL E ++ GLD AI +SKILP+ +I++ ++
Sbjct: 533 LPGCHIILGISNISFGLNPAARQVLNSVFLYESMQVGLDGAIVSASKILPLVKIEEDHQK 592
Query: 624 VALDMVYDRRTED-----YDPLQEFMQLFEGVSAADAKDARAEQLAAMPLFERLAQRIID 678
V D++YDRR D YDPL + +LF G + KD + A++P+ ERL Q IID
Sbjct: 593 VCRDLIYDRREFDGDICTYDPLTKLTELFAGKTT--KKD--PSKTASLPIEERLKQHIID 648
Query: 679 GDKNGLEDDLEAGMKEKSPIAIINEDLLNGMKTVGELFGSGQMQLPFVLQSAETMKTAVA 738
G++ GLED L +K+ P+ IIN LL+GMKTVGELFGSGQMQLPFVLQSA+TMK AVA
Sbjct: 649 GERLGLEDALSEALKQYPPLDIINVFLLDGMKTVGELFGSGQMQLPFVLQSAQTMKAAVA 708
Query: 739 YLEPFMEEEAEATGSAQAEGKGKIVVATVKGDVHDIGKNLVDIILSNNGYDVVNLGIKQP 798
YLEPFM++E G GKGK ++ATVKGDVHDIGKNLVDIILSNNGY V+NLGIKQP
Sbjct: 709 YLEPFMDKE---EGEENDSGKGKFLIATVKGDVHDIGKNLVDIILSNNGYKVINLGIKQP 765
Query: 799 LSAMLEAAEEHKADVIGMSGLLVKSTVVMKENLEEMNNAGASNYPVILGGAALTRTYVEN 858
+ +++A EEH+ D I MSGLLVKST MK+NLE N G + PVILGGAALT +V
Sbjct: 766 VENIIQAYEEHQPDCIAMSGLLVKSTAFMKDNLEVFNERGI-DVPVILGGAALTPKFVYE 824
Query: 859 DLNEVYTGEVYYARDAFEGLRLMDEVMAEKRGEGLD----------PNSPEAIEQAKKKA 908
D Y G+V Y +DAF L MD++M K E D N+ E+ +KA
Sbjct: 825 DCQNTYKGKVVYGKDAFSDLHFMDKLMPAKSAENWDNLQGFLGEFTDNNSLFQEERGEKA 884
Query: 909 ERKARNERSRKIAAERKANAAPVIVPERSDVSTDTPTAAPPFWGTRIVKG--LPLAEFLG 966
KA + + E VI +RS+ A PPFWGT+I+K L E
Sbjct: 885 AEKATEKNGKSSTQE----TPTVIDTKRSEAVEILEPATPPFWGTKILKSNEFDLNEIFW 940
Query: 967 NLDERALFMGQWGLKSTRGNEGPSYEDLVETEGRPRLRYWLDRLKSEGILDHVALVYGYF 1026
LD +AL GQW + + YE + + P L W ++ +E +L H ++YGYF
Sbjct: 941 YLDLQALIAGQWQFRKPKDQSREEYEAFLAEKVYPILEEWKQKVVTENLL-HPTVIYGYF 999
Query: 1027 PAVAEGDDVVILESPDPHAAER---------MRFSFPRQQRGRFLCIADFIRPREQAVKD 1077
P ++ + +++ + A + FPRQ+ GR LCIADF P+E
Sbjct: 1000 PCQSQDNSLLVYDPETIRNANNKIPEDLDPIWKIDFPRQKSGRRLCIADFFSPKE----S 1055
Query: 1078 GQVDVMPFQLVTMGNPIADFANELFAANEYREYLEVHGIGVQLTEALAEYWHSRVRSELK 1137
G++DV P Q VT+G+ ++A +LFAAN+Y YL HG+ VQ EALAE+ H+++R EL
Sbjct: 1056 GKIDVFPMQAVTVGDIATEYAQKLFAANDYTNYLYYHGMAVQTAEALAEWTHAKIRREL- 1114
Query: 1138 LNDGGSVADFDPEDKTKFFDLDYRGARFSFGYGSCPDLEDRAKLVELLEPGRIGVELSEE 1197
AD +P++ + Y+G+R+SFGY +CP+++D+ K +E++ RI + + E
Sbjct: 1115 -----GFADKEPDNIREMLQQHYQGSRYSFGYPACPNIQDQYKQLEVMGCDRINMYMDES 1169
Query: 1198 LQLHPEQSTDAFVLYHPEAKYFN 1220
Q++PEQST A + YHP AKYF+
Sbjct: 1170 EQIYPEQSTTAIIAYHPVAKYFS 1192
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: 3401
Number of extensions: 171
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: 1221
Length of database: 1193
Length adjustment: 47
Effective length of query: 1174
Effective length of database: 1146
Effective search space: 1345404
Effective search space used: 1345404
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_009543124.1 CCE_RS00370 (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.26926.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 1610.5 0.0 0 1610.3 0.0 1.0 1 lcl|NCBI__GCF_000017845.1:WP_009543124.1 CCE_RS00370 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009543124.1 CCE_RS00370 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1610.3 0.0 0 0 2 1181 .. 13 1192 .. 12 1193 .] 0.96
Alignments for each domain:
== domain 1 score: 1610.3 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrgeeadlarelkGnndlLnltkPeviaaihrayfeaGaDive 68
++++lv+DGa Gt lqs+nLt++dF g e++G+n++L++tkPe+++++hr ++e GaD++e
lcl|NCBI__GCF_000017845.1:WP_009543124.1 13 KRPVLVFDGATGTSLQSQNLTADDFGGP------EYEGCNEYLVHTKPEAVEKVHRGFLEVGADVIE 73
689************************5......9******************************** PP
TIGR02082 69 tntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdver 135
t+tF++t+i+la+Ydl+dkay+lnkkaa++a+++a+e++ tpek+RfvaGs+GP++kl+tl+
lcl|NCBI__GCF_000017845.1:WP_009543124.1 74 TDTFGGTSIVLAEYDLADKAYYLNKKAAEIAKKMAAEYS-TPEKPRFVAGSMGPGTKLPTLG----- 134
***************************************.**********************..... PP
TIGR02082 136 pefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvi 202
++++d+l+daY eq++gl+dGG+Dll+iet++D+l++kaal+ave vfe+k+++lPi++s ++
lcl|NCBI__GCF_000017845.1:WP_009543124.1 135 ----HIDFDTLRDAYIEQAEGLYDGGADLLIIETCQDVLQIKAALNAVEAVFEKKRNRLPIMVS-IT 196
....************************************************************.** PP
TIGR02082 203 vdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalg 269
++++G++L+G+++ a+la+le+++i+ilGLnCa+G+++++e++k+lse+++++vs+iPnaGLP+++g
lcl|NCBI__GCF_000017845.1:WP_009543124.1 197 METMGTMLVGTEISAALAILEPYKIDILGLNCATGPEQMKEHIKYLSEHSPFIVSCIPNAGLPENVG 263
******************************************************************9 PP
TIGR02082 270 ...eYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
+Y+ltp el++al++f+e+++++i+GGCCGt+P+hi+a++e +d++p++r+ +e+s++s+++
lcl|NCBI__GCF_000017845.1:WP_009543124.1 264 gqaHYRLTPIELKMALMHFIEDLGVQIIGGCCGTRPDHIKALSELSQDLTPKERHPDYEPSAASIYS 330
999**************************************************************** PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
++++ q++sf+++GeR+n++Gskk+r+l+ aed+++++++ak+qv+eGa++lD+nvD+v++Dg++dm
lcl|NCBI__GCF_000017845.1:WP_009543124.1 331 TQPYIQDNSFLIVGERLNASGSKKCRQLLDAEDWDSLVSLAKSQVKEGAHVLDVNVDYVGRDGVRDM 397
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
++l+s+l+++ i ++PlmlDs+e++++e GLkv++Gk+i+ns++++dGeerFl+ ++l+k+yGa+v
lcl|NCBI__GCF_000017845.1:WP_009543124.1 398 HELASRLVNN--I-TLPLMLDSTEWQKMESGLKVAGGKCILNSTNYEDGEERFLKVLELAKKYGAGV 461
**********..8.***************************************************** PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
vv ++DeeG++rtadkk+eiakRay+++++ +g+p+++i+fDp++l+i+tGiee+++++++++eai+
lcl|NCBI__GCF_000017845.1:WP_009543124.1 462 VVGTIDEEGMGRTADKKFEIAKRAYNAAID-YGIPAHEIFFDPLALPISTGIEEDRENGKATVEAIK 527
*****************************9.************************************ PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
+i+eelP ++i +G+sn+sF+l+ +a+R++l+svFLye++++GlD +iv+a+k++++ +i+++ ++
lcl|NCBI__GCF_000017845.1:WP_009543124.1 528 RIREELPGCHIILGISNISFGLN--PAARQVLNSVFLYESMQVGLDGAIVSASKILPLVKIEEDHQK 592
***********************..****************************************** PP
TIGR02082 602 vvedlildrr.....reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregie 663
v+ dli+drr +++++L++l+el+ g+++k+ ++ ++lp+eeRL++++++Ger g+e
lcl|NCBI__GCF_000017845.1:WP_009543124.1 593 VCRDLIYDRRefdgdICTYDPLTKLTELFAGKTTKK----DPSKTASLPIEERLKQHIIDGERLGLE 655
**********8888779*****************94....55999********************** PP
TIGR02082 664 edleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed 730
++l ea+ k+++pl+ii++ LldGmk+vG+LFGsG+m+LP+v++sa++mk+avayLeP+++ke+ e+
lcl|NCBI__GCF_000017845.1:WP_009543124.1 656 DALSEAL-KQYPPLDIINVFLLDGMKTVGELFGSGQMQLPFVLQSAQTMKAAVAYLEPFMDKEEGEE 721
*******.8999*************************************************997544 PP
TIGR02082 731 ..kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLiv 795
+ kGk+++atvkGDvhDiGkn+vd++Ls+ngy+v++lG+k+Pve+i++a++++++D+i++sGL+v
lcl|NCBI__GCF_000017845.1:WP_009543124.1 722 ndSGKGKFLIATVKGDVHDIGKNLVDIILSNNGYKVINLGIKQPVENIIQAYEEHQPDCIAMSGLLV 788
3399*************************************************************** PP
TIGR02082 796 ksldemvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekk 862
ks+++m+ ++e++++rg+++P++lGGaal++++v +++++Ykg+vvy+kda+++++++dkl+++k+
lcl|NCBI__GCF_000017845.1:WP_009543124.1 789 KSTAFMKDNLEVFNERGIDVPVILGGAALTPKFVYEDCQNTYKGKVVYGKDAFSDLHFMDKLMPAKS 855
******************************************************************8 PP
TIGR02082 863 k..........aeelekikeeyeeirekfgekkeklialsekaarkevfaldrse...dlevpapkf 916
e++++++ +ee ek+ ek ++++ s + + v++++rse le+++p+f
lcl|NCBI__GCF_000017845.1:WP_009543124.1 856 AenwdnlqgflGEFTDNNSLFQEERGEKAAEKATEKNGKSSTQETPTVIDTKRSEaveILEPATPPF 922
89999997776444444444455555555555556666666777788999999995544578899** PP
TIGR02082 917 lGtkvleas...ieellkyiDwkalFv.qWelrgkypkilkdeleglearklfkdakelldklsaek 979
+Gtk+l++ ++e++ y+D++al qW++r+ ++ ++++e+e ++a+k++++++e+++k+++e+
lcl|NCBI__GCF_000017845.1:WP_009543124.1 923 WGTKILKSNefdLNEIFWYLDLQALIAgQWQFRKPKD-QSREEYEAFLAEKVYPILEEWKQKVVTEN 988
*******99999************************9.9**************************** PP
TIGR02082 980 llrargvvGlfPaqsvgddieiytdetvsq...etkpiatvrekleqlrqqsdrylclaDfiaskes 1043
ll++++++G+fP+qs+++ + +y++et+ ++ ++ + k +++rq+s+r+lc+aDf+ +kes
lcl|NCBI__GCF_000017845.1:WP_009543124.1 989 LLHPTVIYGYFPCQSQDNSLLVYDPETIRNannKIPEDLDPIWKIDFPRQKSGRRLCIADFFSPKES 1055
***************************98734344555555678*********************** PP
TIGR02082 1044 GikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeen 1110
G+ D++++++vt+g +a+e+a+kl+a +d++++++ +++a++ aealae++h ++R+el + ++e+
lcl|NCBI__GCF_000017845.1:WP_009543124.1 1056 GKIDVFPMQAVTVGDIATEYAQKLFAANDYTNYLYYHGMAVQTAEALAEWTHAKIRRELGFA-DKEP 1121
***********************************************************998.9*** PP
TIGR02082 1111 ldkedllkerYrGirpafGYpacPdhtekatlleLleaeriGlklteslalaPeasvsglyfahpea 1177
++++++l+++Y+G+r++fGYpacP+ ++++++le++ +ri ++++es++++Pe+s+++++ +hp a
lcl|NCBI__GCF_000017845.1:WP_009543124.1 1122 DNIREMLQQHYQGSRYSFGYPACPNIQDQYKQLEVMGCDRINMYMDESEQIYPEQSTTAIIAYHPVA 1188
******************************************************************* PP
TIGR02082 1178 kYfa 1181
kYf+
lcl|NCBI__GCF_000017845.1:WP_009543124.1 1189 KYFS 1192
***8 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1193 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: 00:00:00.14
# Mc/sec: 9.40
//
[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