Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_020562591.1 A3OW_RS0106365 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000372865.1:WP_020562591.1
Length = 1224
Score = 1659 bits (4296), Expect = 0.0
Identities = 816/1225 (66%), Positives = 1004/1225 (81%), Gaps = 5/1225 (0%)
Query: 3 SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
+K L+ QL +RIL LDG MGTMIQSY+L+E D+RGERFA W DLKGNNDLL L++P
Sbjct: 2 NKTTLLKKQLAQRILFLDGAMGTMIQSYKLDEKDYRGERFAAWDSDLKGNNDLLSLTQPA 61
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I AIH+AY +AGADIIETNTFN+T IAMADY+MESL+ EIN +A+LA A +++ART
Sbjct: 62 IIKAIHSAYLDAGADIIETNTFNATRIAMADYRMESLAYEINLESARLACEAAADYSART 121
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
P KPR+VAGVLGPTNRTAS+SPDVNDP FRNITFD L AY ES + L++GGAD++LIET
Sbjct: 122 PAKPRFVAGVLGPTNRTASMSPDVNDPGFRNITFDELAEAYTESVRGLIDGGADILLIET 181
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
VFDTLNAKAA+FAV+ F+++G +LP+MISGTITDASGRTLSGQT AF++SL+H E ++
Sbjct: 182 VFDTLNAKAAIFAVEQYFDSIGYKLPVMISGTITDASGRTLSGQTVAAFWHSLKHVEPIS 241
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAG 302
FG NCALG ELRQ++ EL+ IA+ +V+AHPNAGLPN FGEYD + MA+++ +WA++G
Sbjct: 242 FGFNCALGARELRQHIDELASIADTHVSAHPNAGLPNEFGEYDETPEAMAEELADWARSG 301
Query: 303 FLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGER 362
+LN++GGCCGTTP HI A+ AV+ PR LP+IP CRLSGLE ++IG DSLFVNVGER
Sbjct: 302 YLNVIGGCCGTTPDHIRAIVAAVQKYPPRALPDIPKECRLSGLEAMSIGRDSLFVNVGER 361
Query: 363 TNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAG 422
TN+TGSA FKRLI E Y ALDVA+QQVENGAQIIDINMDEGMLD++ AMVRFL LIA
Sbjct: 362 TNITGSAAFKRLIVEGNYEAALDVAKQQVENGAQIIDINMDEGMLDSKQAMVRFLMLIAA 421
Query: 423 EPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVV 482
EPDIA+VPIM+DSSKW+++E GLKCIQGKGIVNSIS+KEG FI HAK +RRYGAAV+V
Sbjct: 422 EPDIAKVPIMLDSSKWEILEAGLKCIQGKGIVNSISLKEGETVFIEHAKRVRRYGAAVIV 481
Query: 483 MAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDF 542
MAFDEQGQADTRARK+EIC RAY+ILT+EVGFPPEDIIFDPNIFA+ATGI+EHNNY DF
Sbjct: 482 MAFDEQGQADTRARKVEICARAYRILTQEVGFPPEDIIFDPNIFAIATGIDEHNNYGLDF 541
Query: 543 IGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQL 602
I A +IK+ LP+AL+SGGVSNVSFSFRGN+PVREAIHAVFLY+AIR GMDMGIVNAGQL
Sbjct: 542 IEATREIKQTLPYALVSGGVSNVSFSFRGNNPVREAIHAVFLYHAIRAGMDMGIVNAGQL 601
Query: 603 AIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKR 662
AIY+D+P +LRDAVE V+LN TE LLE+AEKYR + + A + EWRSW V +R
Sbjct: 602 AIYEDIPPDLRDAVETVVLNLHSGATEALLEMAEKYRSMGSGEDARQEHLEWRSWPVKQR 661
Query: 663 LEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA 722
LE++LVKGIT++IE+DTE+AR +A +P++VIEGPLMDGMNVVGDLFG GKMFLPQVVKSA
Sbjct: 662 LEHALVKGITDYIEEDTEQARLEADKPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSA 721
Query: 723 RVMKQAVAYLEPFIEASKE-QGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
RVMK+AVAYL PF+EA + + +TNGK+++ATVKGDVHDIGKNIVGVVLQCNNYE++DLG
Sbjct: 722 RVMKKAVAYLMPFMEAEQSGERQTNGKILMATVKGDVHDIGKNIVGVVLQCNNYEVIDLG 781
Query: 782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
VMVPAE+IL+TA+ N D IGLSGLITPSLDEMV++A+EM+RQGF IPLLIGGATTS+AH
Sbjct: 782 VMVPAEQILQTARLENVDAIGLSGLITPSLDEMVHIAREMQRQGFAIPLLIGGATTSRAH 841
Query: 842 TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
TAVKIE NY GPTVYV +ASR VGV +LLS +D+++A R+EY +R +H ++ ++
Sbjct: 842 TAVKIEPNYEGPTVYVADASRAVGVAGSLLSAELKDNYIAGVRQEYREIRDRHKGREAQS 901
Query: 902 PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKY 960
+LE AR N W Y P LGV+ ++ +ETL YIDW+PFF TW LAG+Y
Sbjct: 902 RQHSLEEARRNKAV--WSHYVPVRPSFLGVKVIDHFPLETLVWYIDWSPFFHTWELAGRY 959
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
P+IL+D +VG EA++LF DA ML K+ +E+ L R V+G FPAN GDD+ +Y DE+RT
Sbjct: 960 PKILDDPLVGTEARKLFDDAQVMLKKIISEQWLTARAVIGFFPANSEGDDVILYTDESRT 1019
Query: 1021 HVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQ 1079
+ HLRQQ K G NYCL+DF+AP SG ADY+GAFAVT G+ + FE +
Sbjct: 1020 EQREILRHLRQQNVKAPGRPNYCLSDFIAPAGSGIADYLGAFAVTTGIGIEQKLREFERE 1079
Query: 1080 HDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGY 1139
HDDY+ IM+KALADRLAEAFAEY+H+ VRK +WGYA +EN NE+LI E YQGIRPAPGY
Sbjct: 1080 HDDYSAIMLKALADRLAEAFAEYMHQAVRKDHWGYARDENYDNEQLINETYQGIRPAPGY 1139
Query: 1140 PACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199
PACP+HTEKA ++ELL V ++TG++LTES+AM+P ++VSGWYF+HP+S+Y+ V +I +DQ
Sbjct: 1140 PACPDHTEKAKLFELLNVTENTGIELTESYAMYPASAVSGWYFAHPESQYFNVGKINKDQ 1199
Query: 1200 VEDYARRKGMSVTEVERWLAPNLGY 1224
++DYARRKG+S ERWL+ +L +
Sbjct: 1200 LQDYARRKGISEELAERWLSAHLNH 1224
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: 3664
Number of extensions: 129
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: 1224
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1177
Effective search space: 1388860
Effective search space used: 1388860
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_020562591.1 A3OW_RS0106365 (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.21688.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 1799.9 0.0 0 1799.7 0.0 1.0 1 lcl|NCBI__GCF_000372865.1:WP_020562591.1 A3OW_RS0106365 methionine syntha
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020562591.1 A3OW_RS0106365 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1799.7 0.0 0 0 2 1182 .] 12 1192 .. 11 1192 .. 0.99
Alignments for each domain:
== domain 1 score: 1799.7 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+ril lDGamGt++qs++L+e+d+rge +a + ++lkGnndlL+lt+P +i+aih ay++aGaDi+
lcl|NCBI__GCF_000372865.1:WP_020562591.1 12 AQRILFLDGAMGTMIQSYKLDEKDYRGErFAAWDSDLKGNNDLLSLTQPAIIKAIHSAYLDAGADII 78
79***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdv 133
etntFn+t ia+adY +e++aye+n ++a+la e+a++++ +tp k+RfvaG+lGPtn++a++spdv
lcl|NCBI__GCF_000372865.1:WP_020562591.1 79 ETNTFNATRIAMADYRMESLAYEINLESARLACEAAADYSaRTPAKPRFVAGVLGPTNRTASMSPDV 145
**************************************999************************** PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p+frn+t+del +aY+e+v+gl+dGG+D+lLietvfDtlnakaa+fave+ f++ g +lP++isg
lcl|NCBI__GCF_000372865.1:WP_020562591.1 146 NDPGFRNITFDELAEAYTESVRGLIDGGADILLIETVFDTLNAKAAIFAVEQYFDSIGYKLPVMISG 212
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267
+i+d+sGrtLsGqt++af +sl+h e +++G nCalGa elr+++ el+ +a++ vs++PnaGLPn+
lcl|NCBI__GCF_000372865.1:WP_020562591.1 213 TITDASGRTLSGQTVAAFWHSLKHVEPISFGFNCALGARELRQHIDELASIADTHVSAHPNAGLPNE 279
******************************************************************* PP
TIGR02082 268 lgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglea 334
+geYd+tpe +a++l+++a+ g+ln++GGCCGttP+hirai +av++ pr ++++++++lsglea
lcl|NCBI__GCF_000372865.1:WP_020562591.1 280 FGEYDETPEAMAEELADWARSGYLNVIGGCCGTTPDHIRAIVAAVQKYPPRALPDIPKECRLSGLEA 346
******************************************************************* PP
TIGR02082 335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401
++i+++s fvn+GeRtn++Gs+ f++li +++ye+al++akqqve+Gaqi+Din+De++lD++++m+
lcl|NCBI__GCF_000372865.1:WP_020562591.1 347 MSIGRDSLFVNVGERTNITGSAAFKRLIVEGNYEAALDVAKQQVENGAQIIDINMDEGMLDSKQAMV 413
******************************************************************* PP
TIGR02082 402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468
++l l+a+epdiakvP+mlDss++e+leaGLk+iqGk+ivnsislk+Ge F+e+ak +++yGaav+
lcl|NCBI__GCF_000372865.1:WP_020562591.1 414 RFLMLIAAEPDIAKVPIMLDSSKWEILEAGLKCIQGKGIVNSISLKEGETVFIEHAKRVRRYGAAVI 480
******************************************************************* PP
TIGR02082 469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535
vmafDe+Gqa+t+++k+ei+ Ray++lt++vgfppediifDpni++iatGi+eh++y++dfiea+re
lcl|NCBI__GCF_000372865.1:WP_020562591.1 481 VMAFDEQGQADTRARKVEICARAYRILTQEVGFPPEDIIFDPNIFAIATGIDEHNNYGLDFIEATRE 547
******************************************************************* PP
TIGR02082 536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602
ik++lP+a +sgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+la+y+di+++lr++
lcl|NCBI__GCF_000372865.1:WP_020562591.1 548 IKQTLPYALVSGGVSNVSFSFRGNNPVREAIHAVFLYHAIRAGMDMGIVNAGQLAIYEDIPPDLRDA 614
******************************************************************* PP
TIGR02082 603 vedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleea 669
ve ++l+ ++ ate Lle+ae+y+ + + +++ +++ ewr++pv++RLe+alvkG++++ieed+e+a
lcl|NCBI__GCF_000372865.1:WP_020562591.1 615 VETVVLNLHSGATEALLEMAEKYRSMGSGEDARQEHLEWRSWPVKQRLEHALVKGITDYIEEDTEQA 681
*****************************9************************************* PP
TIGR02082 670 rkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGk 735
r ++ +pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkavayL+P++e+e++ + +++Gk
lcl|NCBI__GCF_000372865.1:WP_020562591.1 682 RLEADKPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAYLMPFMEAEQSGErQTNGK 748
*********************************************************9865499*** PP
TIGR02082 736 ivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemv 802
i++atvkGDvhDiGkniv+vvL+cn+yev+dlGv+vP+e+il++a+ ++ D iglsGLi++sldemv
lcl|NCBI__GCF_000372865.1:WP_020562591.1 749 ILMATVKGDVHDIGKNIVGVVLQCNNYEVIDLGVMVPAEQILQTARLENVDAIGLSGLITPSLDEMV 815
******************************************************************* PP
TIGR02082 803 evaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelek 869
++a+em+r+g++iPll+GGa++s+ah+avki+++Y+g++vyv das+av v+ +lls++ k+++++
lcl|NCBI__GCF_000372865.1:WP_020562591.1 816 HIAREMQRQGFAIPLLIGGATTSRAHTAVKIEPNYEGPTVYVADASRAVGVAGSLLSAELKDNYIAG 882
******************************************************************* PP
TIGR02082 870 ikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDw 935
+++ey eir +++ ++ + ++ s+++ar++ + +s ++ ++ p flG+kv+++ +e+l+ yiDw
lcl|NCBI__GCF_000372865.1:WP_020562591.1 883 VRQEYREIRDRHKGREAQSRQHSLEEARRN--KAVWS-HYVPVRPSFLGVKVIDHFpLETLVWYIDW 946
***************************955..67899.99*************************** PP
TIGR02082 936 kalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiy 1002
++F +Wel+g+ypkil+d+l+g+earklf+da+ +l+k+++e+ l+ar+v+G+fPa+s+gdd+ +y
lcl|NCBI__GCF_000372865.1:WP_020562591.1 947 SPFFHTWELAGRYPKILDDPLVGTEARKLFDDAQVMLKKIISEQWLTARAVIGFFPANSEGDDVILY 1013
******************************************************************* PP
TIGR02082 1003 tdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkle 1068
tde++ t++ +r+ ++q + +r ++cl+Dfia+ sGi+Dylga++vt+g+g+e+ +++e
lcl|NCBI__GCF_000372865.1:WP_020562591.1 1014 TDESR---TEQREILRHLRQQNVKAPGRpNYCLSDFIAPAGSGIADYLGAFAVTTGIGIEQKLREFE 1077
***99...555556666677777788878************************************** PP
TIGR02082 1069 akeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPd 1135
++ddy++i++kaladrlaea+ae++h+ vRk++wgya++en d+e+l+ e Y+Girpa+GYpacPd
lcl|NCBI__GCF_000372865.1:WP_020562591.1 1078 REHDDYSAIMLKALADRLAEAFAEYMHQAVRKDHWGYARDENYDNEQLINETYQGIRPAPGYPACPD 1144
******************************************************************* PP
TIGR02082 1136 htekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
hteka+l+eLl++ + +G++ltes+a++P+++vsg+yfahpe++Yf+v
lcl|NCBI__GCF_000372865.1:WP_020562591.1 1145 HTEKAKLFELLNVTEnTGIELTESYAMYPASAVSGWYFAHPESQYFNV 1192
***********98766******************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1224 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: 0.12u 0.05s 00:00:00.17 Elapsed: 00:00:00.15
# Mc/sec: 9.05
//
[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