Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_014147029.1 MEALZ_RS02570 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000968535.2:WP_014147029.1
Length = 1223
Score = 1660 bits (4298), Expect = 0.0
Identities = 817/1223 (66%), Positives = 1001/1223 (81%), Gaps = 6/1223 (0%)
Query: 3 SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
SK+E + +L++ IL LDG MGTMIQSY+L E D+RG+RF+DW DLKGNNDLL L++P+
Sbjct: 2 SKLENFKKRLSQSILFLDGAMGTMIQSYKLEEKDYRGKRFSDWTVDLKGNNDLLSLTQPD 61
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I AIH AY + G DIIETNTFN+T IAMADYQMESL+ EIN +A++AR ADE++ +T
Sbjct: 62 IIKAIHCAYLDVGCDIIETNTFNATQIAMADYQMESLAYEINLESARIARQAADEYSQKT 121
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
PEKPR+VAG+LGPTNRTAS+SPDVNDP FRNI FD LV AY E+ + L++GG D+ILIET
Sbjct: 122 PEKPRFVAGILGPTNRTASMSPDVNDPGFRNIDFDTLVDAYTEAMRGLIDGGVDIILIET 181
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
VFDTLNAKAA+FAV FEA+G +LP+MISGTITDASGRTLSGQT AF+NSL H E ++
Sbjct: 182 VFDTLNAKAAIFAVDQYFEAIGYKLPVMISGTITDASGRTLSGQTVAAFWNSLSHIEPIS 241
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAG 302
FG NCALG ELRQ+++ELS IA+ +V+AHPNAGLPN FGEYD + MA ++ +WA G
Sbjct: 242 FGFNCALGAKELRQHIEELSSIADTHVSAHPNAGLPNEFGEYDESPEDMALELADWAANG 301
Query: 303 FLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGER 362
+LNI+GGCCGT+P+HI A+ AV+ PR +P I CRL+GLEP+NIG DSLFVNVGER
Sbjct: 302 YLNIIGGCCGTSPEHIKAIVEAVKQYPPRVVPVIEKQCRLAGLEPMNIGSDSLFVNVGER 361
Query: 363 TNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAG 422
TNVTGSAKFKRL+ E + AL+VA+ QVENGAQIIDINMDEGML+++ AMVRFL+LIA
Sbjct: 362 TNVTGSAKFKRLVVEGDFETALEVAKDQVENGAQIIDINMDEGMLESKEAMVRFLSLIAA 421
Query: 423 EPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVV 482
EPDIA+VPIM+DSSKWD+IE GLKCIQGKGIVNSIS+KEG +AFI HAKL+RRYGAA +V
Sbjct: 422 EPDIAKVPIMLDSSKWDIIEAGLKCIQGKGIVNSISLKEGEEAFIQHAKLIRRYGAAAIV 481
Query: 483 MAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDF 542
MAFDEQGQADTR RK+EIC RAY+ILTE++ FP EDIIFDPNIFA+ATGI+EHNNY DF
Sbjct: 482 MAFDEQGQADTRDRKVEICSRAYRILTEQLNFPAEDIIFDPNIFAIATGIDEHNNYGMDF 541
Query: 543 IGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQL 602
I A +IKR LPHALISGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAGQL
Sbjct: 542 IEATREIKRTLPHALISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKAGMDMGIVNAGQL 601
Query: 603 AIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKR 662
AIY+D+P ELRDAVEDV+LNR D TERLLELAEKYRG + A ++ EWRSW V KR
Sbjct: 602 AIYEDIPLELRDAVEDVVLNRNDHATERLLELAEKYRGDGS-TAAKPEELEWRSWPVTKR 660
Query: 663 LEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA 722
LE++LVKGI +FI++DTE+ARQ+A +P+ VIEG LMDGMNVVGDLFG GKMFLPQVVKSA
Sbjct: 661 LEHALVKGIADFIDEDTEQARQEAEKPLHVIEGALMDGMNVVGDLFGAGKMFLPQVVKSA 720
Query: 723 RVMKQAVAYLEPFIEASKE-QGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
RVMK+AVAYL PF+EA ++ + +TNGK+++ATVKGDVHDIGKNIVGVVLQCNN++++DLG
Sbjct: 721 RVMKKAVAYLMPFMEAEQDGEMQTNGKILMATVKGDVHDIGKNIVGVVLQCNNFQVIDLG 780
Query: 782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
VMVPAEKIL+TA++ D+IGLSGLITPSLDEMV++AKEMERQGF IPL+IGGATTS+AH
Sbjct: 781 VMVPAEKILQTARDEKVDIIGLSGLITPSLDEMVHMAKEMERQGFDIPLMIGGATTSRAH 840
Query: 842 TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
TAVKIE NY GP VYV +ASR+VGV + L+SD ++ F + ++EY+ VR +H +K +T
Sbjct: 841 TAVKIEPNYHGPVVYVADASRSVGVASHLVSDDSKEAFTQKIKEEYKEVRERHQGRKAKT 900
Query: 902 PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKY 960
++E AR N F+W + P LG + ++ ++TL YIDWTPFF TW LAGKY
Sbjct: 901 KQHSIEQARRN--KFNWTDFEPVKPTFLGNKVIDRFPLDTLVWYIDWTPFFHTWELAGKY 958
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
P I ED VVG EA++LF DA ML K+ E+ L R V+G +PAN GDDI +Y+D++R
Sbjct: 959 PNIFEDRVVGEEARKLFDDAQVMLKKIINEEWLQARAVIGFYPANSDGDDIILYKDDSRL 1018
Query: 1021 HVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQ 1079
+ HHLRQQ+ K G NYCL+DF+AP SGK DY+G FAVT G+ +A + FE
Sbjct: 1019 EKREILHHLRQQSVKAPGRPNYCLSDFIAPIDSGKIDYLGGFAVTTGIGIEAKLEEFEKD 1078
Query: 1080 HDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGY 1139
HDDY+ IM+KALADRLAEAFAEY+HE VRK +WGYA +E N+ELI E+YQGIRPAPGY
Sbjct: 1079 HDDYSSIMLKALADRLAEAFAEYMHEAVRKDFWGYAKDEQYRNDELISESYQGIRPAPGY 1138
Query: 1140 PACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199
PACP+HTEK+ ++ELL V TG++LTES+AM+P ++VSGWYFSHP+++Y+ V +I DQ
Sbjct: 1139 PACPDHTEKSKLFELLNVTATTGIELTESYAMYPASAVSGWYFSHPEAQYFNVGKIDHDQ 1198
Query: 1200 VEDYARRKGMSVTEVERWLAPNL 1222
+EDYARRKG++ ERWL+ +L
Sbjct: 1199 LEDYARRKGIAKEVAERWLSAHL 1221
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: 3674
Number of extensions: 133
Number of successful extensions: 6
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: 1223
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1176
Effective search space: 1387680
Effective search space used: 1387680
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_014147029.1 MEALZ_RS02570 (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.23913.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 1822.7 0.1 0 1822.5 0.1 1.0 1 lcl|NCBI__GCF_000968535.2:WP_014147029.1 MEALZ_RS02570 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000968535.2:WP_014147029.1 MEALZ_RS02570 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1822.5 0.1 0 0 2 1182 .] 12 1191 .. 11 1191 .. 0.98
Alignments for each domain:
== domain 1 score: 1822.5 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
++ il lDGamGt++qs++L+e+d+rg+ ++d++ +lkGnndlL+lt+P++i+aih ay++ G Di+
lcl|NCBI__GCF_000968535.2:WP_014147029.1 12 SQSILFLDGAMGTMIQSYKLEEKDYRGKrFSDWTVDLKGNNDLLSLTQPDIIKAIHCAYLDVGCDII 78
799**************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdv 133
etntFn+t+ia+adY++e++aye+n ++a++ar++ade++ +tpek+RfvaG lGPtn++a++spdv
lcl|NCBI__GCF_000968535.2:WP_014147029.1 79 ETNTFNATQIAMADYQMESLAYEINLESARIARQAADEYSqKTPEKPRFVAGILGPTNRTASMSPDV 145
****************************************9************************** PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p+frn+++d+lvdaY+e+++gl+dGGvD++LietvfDtlnakaa+fav + fe+ g +lP++isg
lcl|NCBI__GCF_000968535.2:WP_014147029.1 146 NDPGFRNIDFDTLVDAYTEAMRGLIDGGVDIILIETVFDTLNAKAAIFAVDQYFEAIGYKLPVMISG 212
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267
+i+d+sGrtLsGqt++af +sl+h e +++G nCalGa+elr++++els +a++ vs++PnaGLPn+
lcl|NCBI__GCF_000968535.2:WP_014147029.1 213 TITDASGRTLSGQTVAAFWNSLSHIEPISFGFNCALGAKELRQHIEELSSIADTHVSAHPNAGLPNE 279
******************************************************************* PP
TIGR02082 268 lgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglea 334
+geYd+ pe +a +l+++a++g+lni+GGCCGt Pehi+ai eavk+ pr ++ +e++++l+gle+
lcl|NCBI__GCF_000968535.2:WP_014147029.1 280 FGEYDESPEDMALELADWAANGYLNIIGGCCGTSPEHIKAIVEAVKQYPPRVVPVIEKQCRLAGLEP 346
******************************************************************* PP
TIGR02082 335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401
++i+ +s fvn+GeRtnv+Gs+kf++l+ ++d+e al++ak+qve+Gaqi+Din+De++l+++++m+
lcl|NCBI__GCF_000968535.2:WP_014147029.1 347 MNIGSDSLFVNVGERTNVTGSAKFKRLVVEGDFETALEVAKDQVENGAQIIDINMDEGMLESKEAMV 413
******************************************************************* PP
TIGR02082 402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468
++lsl+a+epdiakvP+mlDss+++++eaGLk+iqGk+ivnsislk+Gee+F+++akli++yGaa++
lcl|NCBI__GCF_000968535.2:WP_014147029.1 414 RFLSLIAAEPDIAKVPIMLDSSKWDIIEAGLKCIQGKGIVNSISLKEGEEAFIQHAKLIRRYGAAAI 480
******************************************************************* PP
TIGR02082 469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535
vmafDe+Gqa+t+d+k+ei++Ray++lte+++fp+ediifDpni++iatGi+eh++y++dfiea+re
lcl|NCBI__GCF_000968535.2:WP_014147029.1 481 VMAFDEQGQADTRDRKVEICSRAYRILTEQLNFPAEDIIFDPNIFAIATGIDEHNNYGMDFIEATRE 547
******************************************************************* PP
TIGR02082 536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602
ik++lP+a isgGvsnvsFs+rgn++vRea+h+vFLy+aikaG+Dmgivnag+la+y+di+ elr++
lcl|NCBI__GCF_000968535.2:WP_014147029.1 548 IKRTLPHALISGGVSNVSFSFRGNNPVREAIHAVFLYHAIKAGMDMGIVNAGQLAIYEDIPLELRDA 614
******************************************************************* PP
TIGR02082 603 vedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleea 669
ved++l+r+++ate+Llelae+y+g ++ +k +e ewr++pv++RLe+alvkG++++i+ed+e+a
lcl|NCBI__GCF_000968535.2:WP_014147029.1 615 VEDVVLNRNDHATERLLELAEKYRGDGSTAAK-PEELEWRSWPVTKRLEHALVKGIADFIDEDTEQA 680
**************************999555.8899****************************** PP
TIGR02082 670 rkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGk 735
r+++++pl++ieg L+dGm+vvGdLFG+GkmfLPqvvksarvmkkavayL+P++e+e++ + +++Gk
lcl|NCBI__GCF_000968535.2:WP_014147029.1 681 RQEAEKPLHVIEGALMDGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLMPFMEAEQDGEmQTNGK 747
*******************************************************998655599*** PP
TIGR02082 736 ivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemv 802
i++atvkGDvhDiGkniv+vvL+cn+++v+dlGv+vP+ekil++a+++k D+iglsGLi++sldemv
lcl|NCBI__GCF_000968535.2:WP_014147029.1 748 ILMATVKGDVHDIGKNIVGVVLQCNNFQVIDLGVMVPAEKILQTARDEKVDIIGLSGLITPSLDEMV 814
******************************************************************* PP
TIGR02082 803 evaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelek 869
+ a+emer+g++iPl++GGa++s+ah+avki+++Y+g+vvyv das++v v+++l+s+++k+++++k
lcl|NCBI__GCF_000968535.2:WP_014147029.1 815 HMAKEMERQGFDIPLMIGGATTSRAHTAVKIEPNYHGPVVYVADASRSVGVASHLVSDDSKEAFTQK 881
******************************************************************* PP
TIGR02082 870 ikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDw 935
ikeey+e+re+++ +k k+++ s+++ar+++ ++++ d e+++p+flG kv++ +++l+ yiDw
lcl|NCBI__GCF_000968535.2:WP_014147029.1 882 IKEEYKEVRERHQGRKAKTKQHSIEQARRNK--FNWT-DFEPVKPTFLGNKVIDRFpLDTLVWYIDW 945
****************************665..6799.99*************************** PP
TIGR02082 936 kalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiy 1002
+++F +Wel+gkyp+i++d+++g+earklf+da+ +l+k+++e+ l+ar+v+G++Pa+s gddi +y
lcl|NCBI__GCF_000968535.2:WP_014147029.1 946 TPFFHTWELAGKYPNIFEDRVVGEEARKLFDDAQVMLKKIINEEWLQARAVIGFYPANSDGDDIILY 1012
******************************************************************* PP
TIGR02082 1003 tdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkle 1068
+d+++ e ++ +++ ++q + +r ++cl+Dfia+ +sG+ Dylg ++vt+g+g+e+ +++e
lcl|NCBI__GCF_000968535.2:WP_014147029.1 1013 KDDSR-LEKRE--ILHHLRQQSVKAPGRpNYCLSDFIAPIDSGKIDYLGGFAVTTGIGIEAKLEEFE 1076
*9998.33333..3322344444455558************************************** PP
TIGR02082 1069 akeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPd 1135
+++ddy+si++kaladrlaea+ae++he vRk++wgya++e+ +++l+ e+Y+Girpa+GYpacPd
lcl|NCBI__GCF_000968535.2:WP_014147029.1 1077 KDHDDYSSIMLKALADRLAEAFAEYMHEAVRKDFWGYAKDEQYRNDELISESYQGIRPAPGYPACPD 1143
******************************************************************* PP
TIGR02082 1136 htekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
htek +l+eLl++ +G++ltes+a++P+++vsg+yf+hpea+Yf+v
lcl|NCBI__GCF_000968535.2:WP_014147029.1 1144 HTEKSKLFELLNVTAtTGIELTESYAMYPASAVSGWYFSHPEAQYFNV 1191
************9988******************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1223 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: 00:00:00.11
# Mc/sec: 12.43
//
[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