Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_029933551.1 N746_RS0101265 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000711195.1:WP_029933551.1
Length = 1239
Score = 1575 bits (4077), Expect = 0.0
Identities = 781/1234 (63%), Positives = 970/1234 (78%), Gaps = 15/1234 (1%)
Query: 4 KVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEV 63
++ QL++ L ER++VLDG MGTMIQ+ +L+E DFRG RFAD+ D+KGNND+LVL++P++
Sbjct: 7 RIAQLKSLLTERVVVLDGAMGTMIQNLQLSEDDFRGARFADYHMDIKGNNDILVLTQPQL 66
Query: 64 IAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTP 123
I IH ++ G D++ETN+FN+TTIA ADY MES +IN AA++AR A E
Sbjct: 67 IRDIHLSFLRQGVDLLETNSFNATTIAQADYDMESQVRDINLHAAQVARE-ACEIAQNED 125
Query: 124 EKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETV 183
KPR+VAGVLGPTNRTASISPDVNDP FRN FD LV AY ++T+AL++GGAD+ILIET+
Sbjct: 126 GKPRFVAGVLGPTNRTASISPDVNDPGFRNTHFDELVEAYVQATQALLDGGADVILIETI 185
Query: 184 FDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTF 243
FDTLNAKAA+FAVK + LG E+PIMISGTITDASGRTLSGQTTEAFYN++RHA+ L+
Sbjct: 186 FDTLNAKAAIFAVKQVEDTLGEEVPIMISGTITDASGRTLSGQTTEAFYNAIRHAKPLSI 245
Query: 244 GLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGF 303
GLNCALGP+ELR YV+ELSRI E +V+ HPNAGLPN FGEYD + MA +++ WA+ G+
Sbjct: 246 GLNCALGPEELRPYVEELSRICETHVSVHPNAGLPNEFGEYDETPEQMAAEVKTWAERGW 305
Query: 304 LNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERT 363
LNI+GGCCGTTP H+AAM++A APR +P + CRLSGLEP+NIGE SLFVNVGER
Sbjct: 306 LNIIGGCCGTTPDHVAAMAKAALAFAPRNIPTPKIECRLSGLEPMNIGETSLFVNVGERN 365
Query: 364 NVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGE 423
NVTGSA FKRLI E+ Y +A+++A +QV +GAQIID+NMDEGML+A+A M RFLN++AGE
Sbjct: 366 NVTGSALFKRLIIEDNYEQAVEIAVKQVNDGAQIIDVNMDEGMLNAKACMTRFLNMMAGE 425
Query: 424 PDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVM 483
PD ARVPIMIDSSKW+ IE GLKCIQGKGIVNSIS+KEG + F+ AK+++RYGAA +VM
Sbjct: 426 PDAARVPIMIDSSKWEAIEAGLKCIQGKGIVNSISLKEGEENFLAQAKMIQRYGAATIVM 485
Query: 484 AFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFI 543
AFDE GQADT RK EIC+R+Y +L GFPPEDIIFDPNIFA+ATGIEEHNNYA DFI
Sbjct: 486 AFDEDGQADTFERKKEICKRSYDLLVAN-GFPPEDIIFDPNIFAIATGIEEHNNYAMDFI 544
Query: 544 GACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLA 603
A + IK+ LPHALISGGVSNVSFSFRGN+PVREAIH+VFLYYAI+ GMDMGIVNA Q+A
Sbjct: 545 NAVDWIKKNLPHALISGGVSNVSFSFRGNNPVREAIHSVFLYYAIQKGMDMGIVNAAQMA 604
Query: 604 IYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAE--WRSWEVNK 661
+YDDL EL+ AVEDV+LN+ +RLLE+AEK+RG D + +++++ WR V K
Sbjct: 605 VYDDLDPELKQAVEDVVLNKDSGAADRLLEVAEKFRG---DGSVQSKESDIRWREASVEK 661
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE+SLVKGIT++IE DTEEAR P++VIEGPLMDGMNVVGDLFG GKMFLPQVVKS
Sbjct: 662 RLEHSLVKGITDYIEDDTEEARTTLGSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKS 721
Query: 722 ARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
ARVMK+AVAYL+P++EA K G+ GK+V+ATVKGDVHDIGKNIVGVVLQCNN++++DLG
Sbjct: 722 ARVMKRAVAYLQPYLEAEKASGQAKGKIVMATVKGDVHDIGKNIVGVVLQCNNFDVIDLG 781
Query: 782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
VMVP EKIL TA + NA++IGLSGLITPSL+EMVNVAKEM+R+G +PLLIGGATTSKAH
Sbjct: 782 VMVPTEKILDTAIKENANVIGLSGLITPSLEEMVNVAKEMQRRGMNLPLLIGGATTSKAH 841
Query: 842 TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
TAVKIE Y P VYV++ASR VGV +L+S+ + D+ A+ R EYE +R + + +
Sbjct: 842 TAVKIEPQYDHPVVYVKDASRAVGVAQSLISNDLKVDYAAKIRAEYEQLREERKARSKQV 901
Query: 902 PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGKY 960
L AR+N DW Y PP LG + + + L + +DW+PFF +W L G Y
Sbjct: 902 KRTPLNKARENPIPVDWTNYVPPKPSFLGTKVFDDIPLTELLDRLDWSPFFQSWDLHGLY 961
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
PRIL+D++VG EA+++F DA ML + EK L R V+G +PAN V DDIE+Y+D++R
Sbjct: 962 PRILDDKLVGEEARKVFADAKTMLQTIIKEKWLTARAVIGFYPANSVVDDIELYKDDSRE 1021
Query: 1021 HVINVSHHLRQQTE-KTGFANYCLADFVAPKLSGK------ADYIGAFAVTGGLEEDALA 1073
V+ H+LRQQ + K G N CL+D++APK + + DYIGAFAVT G+ D
Sbjct: 1022 EVLTRLHNLRQQADKKAGQYNQCLSDYIAPKANKQQPGLVLEDYIGAFAVTAGIGIDEHI 1081
Query: 1074 DAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGI 1133
FEA HDDY IM+KALADRLAEA AEY+HE+VRK +WGYA +E L+NEE+I+E Y+GI
Sbjct: 1082 ARFEAAHDDYQAIMLKALADRLAEALAEYMHEKVRKEFWGYAADEQLTNEEMIKEKYRGI 1141
Query: 1134 RPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVA 1193
RPAPGYPA PEHTEK T+W LL+ + G++LT S+AM P A+VSGWYF+HP+SKY+ V
Sbjct: 1142 RPAPGYPANPEHTEKGTLWSLLKPDSEIGLELTSSYAMTPTAAVSGWYFAHPESKYFGVG 1201
Query: 1194 QIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
I RDQ EDYA+RK ++ E E+WLAPNLGYD +
Sbjct: 1202 SIGRDQAEDYAKRKNWTIQEAEKWLAPNLGYDPE 1235
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: 3748
Number of extensions: 151
Number of successful extensions: 7
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: 1239
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1192
Effective search space: 1406560
Effective search space used: 1406560
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_029933551.1 N746_RS0101265 (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.12619.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 1747.4 0.7 0 1747.2 0.7 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029933551.1 N746_RS0101265 methionine syntha
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711195.1:WP_029933551.1 N746_RS0101265 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1747.2 0.7 0 0 2 1182 .] 16 1200 .. 15 1200 .. 0.98
Alignments for each domain:
== domain 1 score: 1747.2 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+r++vlDGamGt++q+ +L e+dFrg+ +ad++++ kGnnd+L+lt+P++i++ih +++ G D++
lcl|NCBI__GCF_000711195.1:WP_029933551.1 16 TERVVVLDGAMGTMIQNLQLSEDDFRGArFADYHMDIKGNNDILVLTQPQLIRDIHLSFLRQGVDLL 82
68***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etn Fn+t+ia+adYd+e++++++n +aa++are+++ + + k+RfvaG+lGPtn++a++spdv+
lcl|NCBI__GCF_000711195.1:WP_029933551.1 83 ETNSFNATTIAQADYDMESQVRDINLHAAQVAREACEIAQNEDGKPRFVAGVLGPTNRTASISPDVN 149
****************************************9************************** PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p+frn+++delv+aY++++++lldGG+D++Liet+fDtlnakaa+fav++v + g+e+Pi+isg+
lcl|NCBI__GCF_000711195.1:WP_029933551.1 150 DPGFRNTHFDELVEAYVQATQALLDGGADVILIETIFDTLNAKAAIFAVKQVEDTLGEEVPIMISGT 216
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d+sGrtLsGqt+eaf+++++ha+ l++GLnCalG++elr++v+els++ e+ vsv+PnaGLPn++
lcl|NCBI__GCF_000711195.1:WP_029933551.1 217 ITDASGRTLSGQTTEAFYNAIRHAKPLSIGLNCALGPEELRPYVEELSRICETHVSVHPNAGLPNEF 283
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
geYd+tpe++a+++k +ae g lni+GGCCGttP+h++a+a+a+ +pr+ ++ + +++lsgle++
lcl|NCBI__GCF_000711195.1:WP_029933551.1 284 GEYDETPEQMAAEVKTWAERGWLNIIGGCCGTTPDHVAAMAKAALAFAPRNIPTPKIECRLSGLEPM 350
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+i++ s fvn+GeR nv+Gs+ f++li++++ye+a++ia +qv++Gaqi+D+n+De++l+++a m++
lcl|NCBI__GCF_000711195.1:WP_029933551.1 351 NIGETSLFVNVGERNNVTGSALFKRLIIEDNYEQAVEIAVKQVNDGAQIIDVNMDEGMLNAKACMTR 417
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+++a+epd a+vP+m+Dss++e +eaGLk+iqGk+ivnsislk+Gee+Fl +ak+i++yGaa +v
lcl|NCBI__GCF_000711195.1:WP_029933551.1 418 FLNMMAGEPDAARVPIMIDSSKWEAIEAGLKCIQGKGIVNSISLKEGEENFLAQAKMIQRYGAATIV 484
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t ++k ei+kR y+ll++ gfppediifDpni++iatGieeh++ya+dfi+a+ +i
lcl|NCBI__GCF_000711195.1:WP_029933551.1 485 MAFDEDGQADTFERKKEICKRSYDLLVA-NGFPPEDIIFDPNIFAIATGIEEHNNYAMDFINAVDWI 550
***************************9.8************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
k++lP+a isgGvsnvsFs+rgn++vRea+hsvFLy+ai+ G+Dmgivna+++avydd+d+el+++v
lcl|NCBI__GCF_000711195.1:WP_029933551.1 551 KKNLPHALISGGVSNVSFSFRGNNPVREAIHSVFLYYAIQKGMDMGIVNAAQMAVYDDLDPELKQAV 617
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l++++ a ++Lle+ae+++g + +sk + wr+ +ve+RLe++lvkG++++ie+d+eear
lcl|NCBI__GCF_000711195.1:WP_029933551.1 618 EDVVLNKDSGAADRLLEVAEKFRGDGSVQSK-ESDIRWREASVEKRLEHSLVKGITDYIEDDTEEAR 683
**************************99777.66789****************************** PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkiv 737
+l +pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmk+avayL+Pyle+ek++ ++kGkiv
lcl|NCBI__GCF_000711195.1:WP_029933551.1 684 TTLGSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKRAVAYLQPYLEAEKASGQAKGKIV 750
******************************************************************* PP
TIGR02082 738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804
+atvkGDvhDiGkniv+vvL+cn+++v+dlGv+vP+ekil++a k++a+viglsGLi++sl+emv+v
lcl|NCBI__GCF_000711195.1:WP_029933551.1 751 MATVKGDVHDIGKNIVGVVLQCNNFDVIDLGVMVPTEKILDTAIKENANVIGLSGLITPSLEEMVNV 817
******************************************************************* PP
TIGR02082 805 aeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekik 871
a+em+rrg+++Pll+GGa++skah+avki+++Y+ +vvyvkdas+av v+++l+s++ k ++++ki+
lcl|NCBI__GCF_000711195.1:WP_029933551.1 818 AKEMQRRGMNLPLLIGGATTSKAHTAVKIEPQYDHPVVYVKDASRAVGVAQSLISNDLKVDYAAKIR 884
******************************************************************* PP
TIGR02082 872 eeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwka 937
+eye++re+ + + ++++ ++++ar++ + +d++ ++ +p+p flGtkv++++ + ell+ +Dw +
lcl|NCBI__GCF_000711195.1:WP_029933551.1 885 AEYEQLREERKARSKQVKRTPLNKARENPIPVDWT-NYVPPKPSFLGTKVFDDIpLTELLDRLDWSP 950
***********************************.9****************************** PP
TIGR02082 938 lFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytd 1004
+F +W+l+g yp+il+d+l+g+eark+f+dak +l+++++ek l+ar+v+G++Pa+sv ddie+y+d
lcl|NCBI__GCF_000711195.1:WP_029933551.1 951 FFQSWDLHGLYPRILDDKLVGEEARKVFADAKTMLQTIIKEKWLTARAVIGFYPANSVVDDIELYKD 1017
******************************************************************9 PP
TIGR02082 1005 etvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskes....G..ikDylgallvtaglgaeela 1064
+++ ++++ +++ ++q+ ++ ++ ++cl+D+ia+k+ G +Dy+ga++vtag+g++e
lcl|NCBI__GCF_000711195.1:WP_029933551.1 1018 DSR---EEVLTRLHNLRQQADKKAGQyNQCLSDYIAPKANkqqpGlvLEDYIGAFAVTAGIGIDEHI 1081
999...44555555556777777777799********955445652258****************** PP
TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
++ea +ddy++i++kaladrlaealae++he+vRke+wgya++e+l +e+++ke+YrGirpa+GYp
lcl|NCBI__GCF_000711195.1:WP_029933551.1 1082 ARFEAAHDDYQAIMLKALADRLAEALAEYMHEKVRKEFWGYAADEQLTNEEMIKEKYRGIRPAPGYP 1148
******************************************************************* PP
TIGR02082 1132 acPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
a P+htek tl++Ll++++ iGl+lt s+a++P+a+vsg+yfahpe+kYf v
lcl|NCBI__GCF_000711195.1:WP_029933551.1 1149 ANPEHTEKGTLWSLLKPDSeIGLELTSSYAMTPTAAVSGWYFAHPESKYFGV 1200
******************99******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1239 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: 00:00:00.15
# Mc/sec: 9.31
//
[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