Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_085770443.1 B1812_RS03970 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_002117405.1:WP_085770443.1
Length = 1238
Score = 1454 bits (3763), Expect = 0.0
Identities = 734/1225 (59%), Positives = 926/1225 (75%), Gaps = 8/1225 (0%)
Query: 3 SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
S +E L + +ERIL+LDG MGTM+Q ++ +E DFRGERF D DL+GNNDLL+ ++PE
Sbjct: 10 SILEALETRASERILILDGAMGTMVQRHKFSEEDFRGERFKDHHKDLRGNNDLLIFTQPE 69
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
I IH Y AGADIIETNTF++TTIA ADY +E++ +E+N A+LAR +E R
Sbjct: 70 AILEIHRQYLRAGADIIETNTFSATTIAQADYGLEAIVSELNREGARLARRACEE-IGRE 128
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
R+VAG +GPTNRTASISPDV++P FR ++FD L AAY+++ L+EGGAD++L+ET
Sbjct: 129 TGIARFVAGSIGPTNRTASISPDVSNPGFRAVSFDELRAAYKQAALGLIEGGADILLVET 188
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
+FDTLNAKAA+ A++ F+ +G PIMISGTITD SGRTLSGQT AF++SL HA +
Sbjct: 189 IFDTLNAKAAIAALEDAFDEVGTRFPIMISGTITDLSGRTLSGQTARAFWHSLAHARPFS 248
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAG 302
G NCALG E+RQ++ E+ R A+ V A PNAGLPN FG YD + MA+ + E+A++G
Sbjct: 249 IGFNCALGAKEMRQHIVEIGRAADTRVCAFPNAGLPNEFGLYDESPEYMAELVGEFARSG 308
Query: 303 FLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGER 362
+N++GGCCGTTP HIAA+++A +G+APR++PEIP RLSGLEP + D FVNVGER
Sbjct: 309 LVNVLGGCCGTTPDHIAAIAKAAQGVAPREIPEIPPLLRLSGLEPFTLTSDIPFVNVGER 368
Query: 363 TNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAG 422
TNVTGSAKF++LI +Y+ ALDVAR QV NGAQ+ID+NMDEG+LD++ AMV FLNL+A
Sbjct: 369 TNVTGSAKFRKLITAGEYAAALDVARDQVANGAQVIDVNMDEGLLDSKQAMVDFLNLVAA 428
Query: 423 EPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVV 482
EPDIARVP+M+DSSK++VIE GLKC+QGKG+VNSIS+KEG + F A+ + RYGAA+VV
Sbjct: 429 EPDIARVPVMVDSSKFEVIEAGLKCLQGKGVVNSISLKEGEEKFRDEARKVSRYGAAMVV 488
Query: 483 MAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDF 542
MAFDE+GQADT RK+EI +RAYKIL EEVGFPP+DIIFDPNIFAVATGIEEH NY DF
Sbjct: 489 MAFDEKGQADTFERKVEIAKRAYKILVEEVGFPPQDIIFDPNIFAVATGIEEHENYGVDF 548
Query: 543 IGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQL 602
I A + IK +P +SGGVSN+SFSFRGN+PVREA+H+VFLY+AI+ GMDMGIVNAGQL
Sbjct: 549 IEATKAIKEAMPLVHVSGGVSNLSFSFRGNEPVREAMHSVFLYHAIQAGMDMGIVNAGQL 608
Query: 603 AIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKR 662
A+Y+ + ELR+A EDV+LNRR DGTERL+ LAEK++G+ + A WR V KR
Sbjct: 609 AVYEKIDPELREACEDVVLNRRKDGTERLVTLAEKFKGAGA--KREEKDAAWREASVEKR 666
Query: 663 LEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA 722
LEY+LV G+ ++IE D EEAR +TRP++VIEGPLM GMNVVGDLFG+GKMFLPQVVKSA
Sbjct: 667 LEYALVNGVADYIEADVEEARIASTRPLDVIEGPLMAGMNVVGDLFGQGKMFLPQVVKSA 726
Query: 723 RVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGV 782
RVMKQAVA+L P++E K+Q + GK+++ATVKGDVHDIGKNIVGVVL CNN+E++DLGV
Sbjct: 727 RVMKQAVAHLLPYMEKDKDQRSSAGKILLATVKGDVHDIGKNIVGVVLGCNNFEVIDLGV 786
Query: 783 MVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHT 842
M PA KI+ A+ DLIGLSGLITPSLDEM VA E+ER+GF PLLIGGATTS+ HT
Sbjct: 787 MTPAAKIIEMARNEKVDLIGLSGLITPSLDEMCFVASELEREGFETPLLIGGATTSRVHT 846
Query: 843 AVKIEQNY-SGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
AVKI NY G VYV +ASR VGV ALLS T R D+ A+TR EYE V H + +
Sbjct: 847 AVKISPNYRRGQAVYVTDASRAVGVAQALLSAT-RGDYKAKTRDEYERVAEVHAKAQADK 905
Query: 902 PPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKY 960
V + AAR N DW++YTP GV+ + + L YIDWTPFF TW G++
Sbjct: 906 NRVPIAAARANAAKLDWESYTPTKPTFTGVRGFASYDVAELIPYIDWTPFFSTWEFKGRF 965
Query: 961 PRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRT 1020
P +L+D G A+ L+ DA MLD++ AE+ P+ +G +PAN VGDDI +Y E+R
Sbjct: 966 PALLDDPARGEAARTLYDDARAMLDRIVAERWFTPKAAIGFWPANSVGDDIALYTGESRQ 1025
Query: 1021 HVINVSHHLRQQTEKTGF-ANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQ 1079
+ + LRQQ + G N LADFVAP+ SGKADYIGAF VT G EE ++ +
Sbjct: 1026 ERLATLYTLRQQLPRQGARPNLALADFVAPEGSGKADYIGAFVVTAGAEEAKISARYARA 1085
Query: 1080 HDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGY 1139
+DDY IMVKALADR+ EA AE +HERVR+ +WGYA ENL+ +EL+ E YQGIRPAPGY
Sbjct: 1086 NDDYGSIMVKALADRIVEALAERMHERVRREFWGYAAAENLAPQELMGEPYQGIRPAPGY 1145
Query: 1140 PACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199
PA P+H+EKAT++ LL E+ TG KLTE+FAM P +++ G Y +HP++ Y+ V++++RDQ
Sbjct: 1146 PAQPDHSEKATLFRLLSAER-TGAKLTETFAMSPPSTICGVYIAHPEAHYFGVSKVERDQ 1204
Query: 1200 VEDYARRKGMSVTEVERWLAPNLGY 1224
VEDYARRKG+ V E+ERWLAP L Y
Sbjct: 1205 VEDYARRKGVPVAEMERWLAPVLNY 1229
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: 3603
Number of extensions: 138
Number of successful extensions: 9
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: 1238
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1191
Effective search space: 1405380
Effective search space used: 1405380
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_085770443.1 B1812_RS03970 (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.3936.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 1734.1 0.0 0 1733.9 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085770443.1 B1812_RS03970 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002117405.1:WP_085770443.1 B1812_RS03970 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1733.9 0.0 0 0 2 1182 .] 20 1197 .. 19 1197 .. 0.99
Alignments for each domain:
== domain 1 score: 1733.9 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
++ril+lDGamGt++q+++ e+dFrge ++d++++l+GnndlL t+Pe+i +ihr+y+ aGaDi+
lcl|NCBI__GCF_002117405.1:WP_085770443.1 20 SERILILDGAMGTMVQRHKFSEEDFRGErFKDHHKDLRGNNDLLIFTQPEAILEIHRQYLRAGADII 86
68***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etntF++t+ia+adY+le+ + eln+++a+lar++++e+++++ RfvaGs+GPtn++a++spdv
lcl|NCBI__GCF_002117405.1:WP_085770443.1 87 ETNTFSATTIAQADYGLEAIVSELNREGARLARRACEEIGRETGIARFVAGSIGPTNRTASISPDVS 153
******************************************************************* PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p+fr v +del++aYk+++ gl++GG+D+lL+et+fDtlnakaa+ a+e++f+e g++ Pi+isg+
lcl|NCBI__GCF_002117405.1:WP_085770443.1 154 NPGFRAVSFDELRAAYKQAALGLIEGGADILLVETIFDTLNAKAAIAALEDAFDEVGTRFPIMISGT 220
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d sGrtLsGqt af +sl ha +++G nCalGa+e+r+++ e+++ a++ v ++PnaGLPn++
lcl|NCBI__GCF_002117405.1:WP_085770443.1 221 ITDLSGRTLSGQTARAFWHSLAHARPFSIGFNCALGAKEMRQHIVEIGRAADTRVCAFPNAGLPNEF 287
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g Yd+ pe +a+ + efa+ gl+n++GGCCGttP+hi+aia+a+++++pr+ +e+++ ++lsgle++
lcl|NCBI__GCF_002117405.1:WP_085770443.1 288 GLYDESPEYMAELVGEFARSGLVNVLGGCCGTTPDHIAAIAKAAQGVAPREIPEIPPLLRLSGLEPF 354
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+++ + fvn+GeRtnv+Gs+kfrkli+a++y +al++a++qv +Gaq++D+n+De+llD++++m+
lcl|NCBI__GCF_002117405.1:WP_085770443.1 355 TLTSDIPFVNVGERTNVTGSAKFRKLITAGEYAAALDVARDQVANGAQVIDVNMDEGLLDSKQAMVD 421
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+a+epdia+vP+m+Dss+fev+eaGLk++qGk++vnsislk+Gee+F ++a+++ +yGaa+vv
lcl|NCBI__GCF_002117405.1:WP_085770443.1 422 FLNLVAAEPDIARVPVMVDSSKFEVIEAGLKCLQGKGVVNSISLKEGEEKFRDEARKVSRYGAAMVV 488
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t ++k+eiakRayk+l+e+vgfpp+diifDpni+++atGieeh++y++dfiea++ i
lcl|NCBI__GCF_002117405.1:WP_085770443.1 489 MAFDEKGQADTFERKVEIAKRAYKILVEEVGFPPQDIIFDPNIFAVATGIEEHENYGVDFIEATKAI 555
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
ke +P +++sgGvsn+sFs+rgn++vRea+hsvFLy+ai+aG+Dmgivnag+lavy++id+elre++
lcl|NCBI__GCF_002117405.1:WP_085770443.1 556 KEAMPLVHVSGGVSNLSFSFRGNEPVREAMHSVFLYHAIQAGMDMGIVNAGQLAVYEKIDPELREAC 622
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l+rr++ te+L++lae++kg +k +e++ a+wr+ +ve+RLe+alv+G++++ie+d+eear
lcl|NCBI__GCF_002117405.1:WP_085770443.1 623 EDVVLNRRKDGTERLVTLAEKFKGAGAK--REEKDAAWREASVEKRLEYALVNGVADYIEADVEEAR 687
****************************..7789********************************* PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkiv 737
++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L Py+ek+k++ +s+Gki+
lcl|NCBI__GCF_002117405.1:WP_085770443.1 688 IASTRPLDVIEGPLMAGMNVVGDLFGQGKMFLPQVVKSARVMKQAVAHLLPYMEKDKDQRSSAGKIL 754
******************************************************************* PP
TIGR02082 738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804
latvkGDvhDiGkniv+vvL+cn++ev+dlGv++P++ki+e+a+++k D+iglsGLi++sldem +v
lcl|NCBI__GCF_002117405.1:WP_085770443.1 755 LATVKGDVHDIGKNIVGVVLGCNNFEVIDLGVMTPAAKIIEMARNEKVDLIGLSGLITPSLDEMCFV 821
******************************************************************* PP
TIGR02082 805 aeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkkaeeleki 870
a e+er+g+++Pll+GGa++s+ h+avki ++Y+ g+ vyv+das+av v+++lls+++ ++ +k+
lcl|NCBI__GCF_002117405.1:WP_085770443.1 822 ASELEREGFETPLLIGGATTSRVHTAVKISPNYRrGQAVYVTDASRAVGVAQALLSATR-GDYKAKT 887
*********************************6489*********************6.7899*** PP
TIGR02082 871 keeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwk 936
++eye + e + + + ++ ++++aar + +ld++ +++++p+f G++ + ++ ++el++yiDw+
lcl|NCBI__GCF_002117405.1:WP_085770443.1 888 RDEYERVAEVHAKAQADKNRVPIAAARANAAKLDWE-SYTPTKPTFTGVRGFASYdVAELIPYIDWT 953
************************************.9***************************** PP
TIGR02082 937 alFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiyt 1003
++F +We++g++p l+d+ +g+ ar l++da+++ld+++ae+ ++++ +G++Pa+svgddi++yt
lcl|NCBI__GCF_002117405.1:WP_085770443.1 954 PFFSTWEFKGRFPALLDDPARGEAARTLYDDARAMLDRIVAERWFTPKAAIGFWPANSVGDDIALYT 1020
******************************************************************* PP
TIGR02082 1004 detvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakklea 1069
+e++ ++ +at+++ ++ql +q +r +l+laDf+a+ sG++Dy+ga++vtag ++++++ ++
lcl|NCBI__GCF_002117405.1:WP_085770443.1 1021 GESR---QERLATLYTLRQQLPRQGARpNLALADFVAPEGSGKADYIGAFVVTAGAEEAKISARYAR 1084
9999...566777777666666666666*************************************** PP
TIGR02082 1070 keddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdh 1136
+ddy+si+vkaladr+ ealae +hervR+e+wgya+ enl+ ++l+ e Y+Girpa+GYpa+Pdh
lcl|NCBI__GCF_002117405.1:WP_085770443.1 1085 ANDDYGSIMVKALADRIVEALAERMHERVRREFWGYAAAENLAPQELMGEPYQGIRPAPGYPAQPDH 1151
******************************************************************* PP
TIGR02082 1137 tekatlleLleaeriGlklteslalaPeasvsglyfahpeakYfav 1182
+ekatl++Ll+aer+G klte +a+ P ++++g+y+ahpea+Yf v
lcl|NCBI__GCF_002117405.1:WP_085770443.1 1152 SEKATLFRLLSAERTGAKLTETFAMSPPSTICGVYIAHPEAHYFGV 1197
********************************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1238 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: 0.08u 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 13.85
//
[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