Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_019865328.1 METMI_RS0105835 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000384075.1:WP_019865328.1
Length = 1225
Score = 1651 bits (4275), Expect = 0.0
Identities = 821/1226 (66%), Positives = 996/1226 (81%), Gaps = 10/1226 (0%)
Query: 3 SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
+K + L+ L++RIL LDG MGTMIQSY+L E D+RG RFA+W DLKGNNDLL L++P+
Sbjct: 2 NKTKLLKQLLSQRILFLDGAMGTMIQSYKLEEKDYRGSRFANWDVDLKGNNDLLTLTQPD 61
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I AIH+AYFEAG DI+ETNTFNS +I M DY ME+L E+N AKLA+ ADE+T +T
Sbjct: 62 IIKAIHSAYFEAGTDIVETNTFNSNSIGMGDYGMEALVYELNVEGAKLAKQAADEYTQKT 121
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
P KPR+VAGVLGPT+RTAS+SPDVNDP FRNI+FD LV Y E+T+ L++GGAD+ILIET
Sbjct: 122 PGKPRFVAGVLGPTSRTASMSPDVNDPGFRNISFDELVVTYTEATRGLIDGGADIILIET 181
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
+FDTLNAKAA FAV+ F+ G +LP+MISGTITDASGRTLSGQT AF++SL+H ++
Sbjct: 182 IFDTLNAKAAAFAVENVFDTFGYKLPVMISGTITDASGRTLSGQTVAAFWHSLKHINPIS 241
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAG 302
FG NCALG ELRQ+++ELS IA +V+AHPNAGLPNAFGEYD + MA +I +WA +G
Sbjct: 242 FGFNCALGAKELRQHIEELSTIANTHVSAHPNAGLPNAFGEYDESPEAMAAEIEDWAVSG 301
Query: 303 FLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGER 362
+LNI+GGCCGT+P HI A+ AV+ PR +P++P C LSGLE ++IG DSLFVNVGER
Sbjct: 302 YLNIIGGCCGTSPAHIKAIVEAVQKHPPRTIPDLPKKCLLSGLEAMSIGPDSLFVNVGER 361
Query: 363 TNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAG 422
TNVTGSA FKRLI E + ALDVARQQVENGAQIIDINMDEGML+++ AMVRFL LIA
Sbjct: 362 TNVTGSAVFKRLIIEGNFEAALDVARQQVENGAQIIDINMDEGMLESKEAMVRFLMLIAS 421
Query: 423 EPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVV 482
EPDIA+VPIM+DSSKWD++E GLKCIQGKGIVNSISMKEG +AFI HAKL++RYGAAV+V
Sbjct: 422 EPDIAKVPIMLDSSKWDILEAGLKCIQGKGIVNSISMKEGEEAFIKHAKLVKRYGAAVIV 481
Query: 483 MAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDF 542
MAFDE GQADT+ARK+EIC RAYKIL ++GFPPEDIIFDPNIFAVATGIEEHNNY DF
Sbjct: 482 MAFDEAGQADTQARKVEICTRAYKILVGQIGFPPEDIIFDPNIFAVATGIEEHNNYGVDF 541
Query: 543 IGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQL 602
I A IK+ LPHAL+SGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GM MGIVNAGQL
Sbjct: 542 IEATRTIKQTLPHALVSGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMSMGIVNAGQL 601
Query: 603 AIYDDLPAELRDAVEDVILNRRD-DGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
AIY+D+P +LRDAVEDVILNR D GTE+LLELAEKYRG + + A ++ EWRSW V+K
Sbjct: 602 AIYEDIPLDLRDAVEDVILNRHDGSGTEKLLELAEKYRGDGSTNEAKPEEQEWRSWPVSK 661
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LVKGIT+FI++DTE ARQ+A RP+ VIEGPLMDGMNVVGDLFG GKMFLPQVVKS
Sbjct: 662 RLEHALVKGITDFIDEDTEAARQEAERPLHVIEGPLMDGMNVVGDLFGAGKMFLPQVVKS 721
Query: 722 ARVMKQAVAYLEPFIEASKEQG--KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVD 779
ARVMK+AVAYL P++EA K G +TNGK+++ATVKGDVHDIGKNIVGVVLQCNNY+++D
Sbjct: 722 ARVMKKAVAYLMPYMEADKVAGDRQTNGKILMATVKGDVHDIGKNIVGVVLQCNNYDVID 781
Query: 780 LGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSK 839
LGVMVP EKIL++A+ N D+IGLSGLITPSLDEMV+VAKEM+RQGFTIPL+IGGATTS+
Sbjct: 782 LGVMVPTEKILQSARLENVDIIGLSGLITPSLDEMVHVAKEMQRQGFTIPLMIGGATTSR 841
Query: 840 AHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
AHTAVKIE NY+G TVYV +ASR VGV + LLS + +FV R EY VR +H K+
Sbjct: 842 AHTAVKIEPNYTGTTVYVTDASRAVGVASNLLSTDLKAEFVEGLRGEYAEVRERHKGKES 901
Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHR-LGVQEV-EASIETLRNYIDWTPFFMTWSLA 957
+T ++EAAR N F + Y PV + LGV+ + + S+ TL +IDW+PFF TW +A
Sbjct: 902 KTKQHSIEAARANKF----RGYHQPVKPKFLGVKVIDDVSLATLAEFIDWSPFFQTWEMA 957
Query: 958 GKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDE 1017
G YP+IL+DEV+G EA++LF DA ML ++ AE L R VVG FPA DD+ +Y DE
Sbjct: 958 GSYPKILQDEVIGSEARKLFADAQAMLKQIVAENWLGARAVVGFFPAYSDEDDVILYTDE 1017
Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
R+ V+ HHLRQQ K G NYCL+DF+APK SG ADY+G FAVT G+ + F
Sbjct: 1018 NRSEVLETLHHLRQQNVKAPGRPNYCLSDFIAPKSSGVADYLGGFAVTTGIGIETKLAEF 1077
Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
A +DDY+ IM+KALADRLAEAFAEYLH RVRK +WGY +EN N +LI E YQGIRPA
Sbjct: 1078 AADNDDYSSIMLKALADRLAEAFAEYLHLRVRKEFWGYVEDENHDNSQLINEAYQGIRPA 1137
Query: 1137 PGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQ 1196
PGYPACP+HTEKA ++ELL+V +HT ++LTES+AM+P ++VSGWYFSHP+S+Y+ V +I
Sbjct: 1138 PGYPACPDHTEKAKLFELLKVTEHTTIELTESYAMYPASAVSGWYFSHPESQYFNVGKID 1197
Query: 1197 RDQVEDYARRKGMSVTEVERWLAPNL 1222
+DQ++DYARRKG++ RWLA +L
Sbjct: 1198 KDQLQDYARRKGIAEEVAARWLAAHL 1223
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: 3651
Number of extensions: 140
Number of successful extensions: 5
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: 1225
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1178
Effective search space: 1390040
Effective search space used: 1390040
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_019865328.1 METMI_RS0105835 (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.23020.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 1803.2 0.1 0 1803.1 0.1 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019865328.1 METMI_RS0105835 methionine synth
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019865328.1 METMI_RS0105835 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1803.1 0.1 0 0 1 1182 [] 11 1193 .. 11 1193 .. 0.99
Alignments for each domain:
== domain 1 score: 1803.1 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++ril lDGamGt++qs++L+e+d+rg+ +a++ +lkGnndlL+lt+P++i+aih ayfeaG Di
lcl|NCBI__GCF_000384075.1:WP_019865328.1 11 LSQRILFLDGAMGTMIQSYKLEEKDYRGSrFANWDVDLKGNNDLLTLTQPDIIKAIHSAYFEAGTDI 77
589**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspd 132
vetntFns++i ++dY++e+++yeln ++akla+++ade+t +tp k+RfvaG+lGPt+++a++spd
lcl|NCBI__GCF_000384075.1:WP_019865328.1 78 VETNTFNSNSIGMGDYGMEALVYELNVEGAKLAKQAADEYTqKTPGKPRFVAGVLGPTSRTASMSPD 144
*****************************************99************************ PP
TIGR02082 133 verpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilis 199
v++p+frn+ +delv Y+e+++gl+dGG+D++Liet+fDtlnakaa fave+vf+ g +lP++is
lcl|NCBI__GCF_000384075.1:WP_019865328.1 145 VNDPGFRNISFDELVVTYTEATRGLIDGGADIILIETIFDTLNAKAAAFAVENVFDTFGYKLPVMIS 211
******************************************************************* PP
TIGR02082 200 gvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPn 266
g+i+d+sGrtLsGqt++af +sl+h + +++G nCalGa+elr++++els +a++ vs++PnaGLPn
lcl|NCBI__GCF_000384075.1:WP_019865328.1 212 GTITDASGRTLSGQTVAAFWHSLKHINPISFGFNCALGAKELRQHIEELSTIANTHVSAHPNAGLPN 278
******************************************************************* PP
TIGR02082 267 algeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgle 333
a+geYd+ pe +a++++++a g+lni+GGCCGt P+hi+ai eav++ pr ++l++k++lsgle
lcl|NCBI__GCF_000384075.1:WP_019865328.1 279 AFGEYDESPEAMAAEIEDWAVSGYLNIIGGCCGTSPAHIKAIVEAVQKHPPRTIPDLPKKCLLSGLE 345
******************************************************************* PP
TIGR02082 334 alkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadm 400
a++i+++s fvn+GeRtnv+Gs+ f++li+++++e+al++a+qqve+Gaqi+Din+De++l+++++m
lcl|NCBI__GCF_000384075.1:WP_019865328.1 346 AMSIGPDSLFVNVGERTNVTGSAVFKRLIIEGNFEAALDVARQQVENGAQIIDINMDEGMLESKEAM 412
******************************************************************* PP
TIGR02082 401 kkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaav 467
+++l l+asepdiakvP+mlDss++++leaGLk+iqGk+ivnsis+k+Gee+F+++akl+k+yGaav
lcl|NCBI__GCF_000384075.1:WP_019865328.1 413 VRFLMLIASEPDIAKVPIMLDSSKWDILEAGLKCIQGKGIVNSISMKEGEEAFIKHAKLVKRYGAAV 479
******************************************************************* PP
TIGR02082 468 vvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieair 534
+vmafDe Gqa+t+++k+ei++Rayk+l+ ++gfppediifDpni+++atGieeh++y++dfiea+r
lcl|NCBI__GCF_000384075.1:WP_019865328.1 480 IVMAFDEAGQADTQARKVEICTRAYKILVGQIGFPPEDIIFDPNIFAVATGIEEHNNYGVDFIEATR 546
******************************************************************* PP
TIGR02082 535 eikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelre 601
+ik++lP+a +sgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+ mgivnag+la+y+di+ +lr+
lcl|NCBI__GCF_000384075.1:WP_019865328.1 547 TIKQTLPHALVSGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMSMGIVNAGQLAIYEDIPLDLRD 613
******************************************************************* PP
TIGR02082 602 vvedlildrr.reatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedle 667
+ved+il+r+ + tekLlelae+y+g ++++++ +e+ewr++pv++RLe+alvkG++++i+ed+e
lcl|NCBI__GCF_000384075.1:WP_019865328.1 614 AVEDVILNRHdGSGTEKLLELAEKYRGDGSTNEAKPEEQEWRSWPVSKRLEHALVKGITDFIDEDTE 680
*********83578*****************9*********************************** PP
TIGR02082 668 earkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed..ks 732
+ar+++++pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkavayL+Py+e++k + ++
lcl|NCBI__GCF_000384075.1:WP_019865328.1 681 AARQEAERPLHVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLMPYMEADKVAGdrQT 747
***********************************************************98765699 PP
TIGR02082 733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799
+Gki++atvkGDvhDiGkniv+vvL+cn+y+v+dlGv+vP+ekil+ a+ ++ D+iglsGLi++sld
lcl|NCBI__GCF_000384075.1:WP_019865328.1 748 NGKILMATVKGDVHDIGKNIVGVVLQCNNYDVIDLGVMVPTEKILQSARLENVDIIGLSGLITPSLD 814
******************************************************************* PP
TIGR02082 800 emvevaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaee 866
emv+va+em+r+g++iPl++GGa++s+ah+avki+++Y g++vyv+das+av v+++lls + kae+
lcl|NCBI__GCF_000384075.1:WP_019865328.1 815 EMVHVAKEMQRQGFTIPLMIGGATTSRAHTAVKIEPNYTGTTVYVTDASRAVGVASNLLSTDLKAEF 881
******************************************************************* PP
TIGR02082 867 lekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellky 932
+e ++ ey e+re+++ k++k+++ s++aar ++f ++ +++pkflG+kv++++ +++l ++
lcl|NCBI__GCF_000384075.1:WP_019865328.1 882 VEGLRGEYAEVRERHKGKESKTKQHSIEAARANKFRGYHQ----PVKPKFLGVKVIDDVsLATLAEF 944
*******************************999987766....9********************** PP
TIGR02082 933 iDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddi 999
iDw ++F +We++g+ypkil+de+ g earklf+da+++l++++ae+ l ar+vvG+fPa s +dd+
lcl|NCBI__GCF_000384075.1:WP_019865328.1 945 IDWSPFFQTWEMAGSYPKILQDEVIGSEARKLFADAQAMLKQIVAENWLGARAVVGFFPAYSDEDDV 1011
******************************************************************* PP
TIGR02082 1000 eiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelak 1065
+ytde + +++ t+++ ++q + +r ++cl+Dfia+k+sG +Dylg ++vt+g+g+e
lcl|NCBI__GCF_000384075.1:WP_019865328.1 1012 ILYTDENR---SEVLETLHHLRQQNVKAPGRpNYCLSDFIAPKSSGVADYLGGFAVTTGIGIETKLA 1075
*****999...566666666667777777778********************************99* PP
TIGR02082 1066 kleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpa 1132
++ a++ddy+si++kaladrlaea+ae+lh rvRke+wgy e+en+d+++l+ e Y+Girpa+GYpa
lcl|NCBI__GCF_000384075.1:WP_019865328.1 1076 EFAADNDDYSSIMLKALADRLAEAFAEYLHLRVRKEFWGYVEDENHDNSQLINEAYQGIRPAPGYPA 1142
******************************************************************* PP
TIGR02082 1133 cPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
cPdhteka+l+eLl++ + + ++ltes+a++P+++vsg+yf+hpe++Yf+v
lcl|NCBI__GCF_000384075.1:WP_019865328.1 1143 CPDHTEKAKLFELLKVTEhTTIELTESYAMYPASAVSGWYFSHPESQYFNV 1193
**************98776******************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1225 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: 0.06u 0.04s 00:00:00.10 Elapsed: 00:00:00.10
# Mc/sec: 13.23
//
[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