Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_019894932.1 A377_RS0104280 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000384235.1:WP_019894932.1
Length = 1253
Score = 1593 bits (4125), Expect = 0.0
Identities = 790/1236 (63%), Positives = 981/1236 (79%), Gaps = 17/1236 (1%)
Query: 3 SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
+++ QLR +L RI+ LDG MGTMIQ+ +L E++FRGERF+DW CD++GNND+L +++P+
Sbjct: 20 TRIAQLRDRLKTRIVRLDGAMGTMIQNLKLTESEFRGERFSDWSCDIQGNNDILAMTQPQ 79
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I IH + +AGADI+ETN+FN+TTIA ADY+MES+ ++N AAA++AR D T +
Sbjct: 80 LIENIHRQFLQAGADIVETNSFNATTIAQADYEMESIVTDLNIAAAEVARRACDALTDQD 139
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
E PR+VAGVLGPTNRTASISPDVNDP RN TFD LV AY ++T+AL+ GGAD+ILIET
Sbjct: 140 GE-PRFVAGVLGPTNRTASISPDVNDPGARNTTFDQLVEAYEQATRALITGGADVILIET 198
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
+FDTLNAKAA+FAVK LG E+PIM+SGTITDASGRTLSGQTTEAFYN++ HA L+
Sbjct: 199 IFDTLNAKAAIFAVKNIETELGDEIPIMLSGTITDASGRTLSGQTTEAFYNAVSHANPLS 258
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAG 302
GLNCALGP+ELR+YV ELSR+ E YV+ HPNAGLPN FGEYD + MA +I WA+ G
Sbjct: 259 VGLNCALGPEELRRYVGELSRVCEAYVSIHPNAGLPNEFGEYDESPEQMAHEIAIWAEKG 318
Query: 303 FLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGER 362
++NI+GGCCGTTP HIAA ++A++ PR LPEI ACRLSGLEPLNI EDSLFVNVGER
Sbjct: 319 WINIIGGCCGTTPDHIAAFTQAMKNHTPRALPEIAPACRLSGLEPLNIDEDSLFVNVGER 378
Query: 363 TNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAG 422
NVTGSAKFKRLI E+ + EA+D+A +QVE+GAQ+ID+NMDEGMLDA+A MV+FLNL+A
Sbjct: 379 NNVTGSAKFKRLIIEDNFDEAIDIAVKQVEDGAQVIDVNMDEGMLDAKACMVKFLNLLAS 438
Query: 423 EPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVV 482
EPD +RVPIMIDSSKW+VIE GLKCIQGKGIVNSIS+KEG +AFI AKL+R YGAA ++
Sbjct: 439 EPDASRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISLKEGEEAFIKQAKLVRDYGAAAII 498
Query: 483 MAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDF 542
MAFDE GQADT RKIEIC R+Y++L ++VGFPP+DIIFDPNIFAVATGIEEHN Y DF
Sbjct: 499 MAFDEDGQADTYERKIEICERSYRVLVDKVGFPPQDIIFDPNIFAVATGIEEHNRYGLDF 558
Query: 543 IGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQL 602
I A IK+ LPHA ISGGVSNVSFSFRGN+PVREAIH+VFLYYAI+ GMDMGIVNAGQ+
Sbjct: 559 IEAVRWIKQHLPHAKISGGVSNVSFSFRGNNPVREAIHSVFLYYAIKEGMDMGIVNAGQM 618
Query: 603 AIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAE--WRSWEVN 660
AIYD++P +LRDAVEDVILN+ + +ERLLE+AE+YRG D TA +++A+ WR +V
Sbjct: 619 AIYDEVPPKLRDAVEDVILNKDPEASERLLEIAEEYRG---DGTAASREADLTWREGDVE 675
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
RL+++L+KGIT++IE DTEEA Q+ PI VIEGPLMDGMN+VGDLFG GKMFLPQVVK
Sbjct: 676 SRLQHALIKGITDYIEDDTEEAYQKLGAPINVIEGPLMDGMNIVGDLFGAGKMFLPQVVK 735
Query: 721 SARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
SARVMK+AVA+L+P+++A K +G+ GK+V+ATVKGDVHDIGKNIVG+VLQCNN++++DL
Sbjct: 736 SARVMKRAVAHLDPYLQAEKAEGQVKGKIVLATVKGDVHDIGKNIVGIVLQCNNFDVIDL 795
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVP E IL A++ NA+++GLSGLITPSL+EMVNVAK M+ +G +PLLIGGATTSKA
Sbjct: 796 GVMVPGEDILDAAEKENANVVGLSGLITPSLEEMVNVAKMMQERGMEVPLLIGGATTSKA 855
Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
HTAVKIE Y P VYV++ASR VGV +L+S ++ F + R EY VR +
Sbjct: 856 HTAVKIEPQYEHPVVYVKDASRAVGVAQSLISHDKKAAFADKIRAEYADVREARKARAKE 915
Query: 901 TPPVTLEAARDN-------DFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFM 952
V+++ AR N D A W +TP LG + +E +ETL DW+PFF
Sbjct: 916 VKRVSIKQARQNPALKTLDDQA--WSDFTPTKPSFLGSRVIEDFPLETLLERFDWSPFFQ 973
Query: 953 TWSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIE 1012
W L GKYPRIL+D+VVG EA+++F DA +ML+ L EK L + V G +PANRVGDDIE
Sbjct: 974 AWELHGKYPRILDDKVVGEEAKKVFADAKEMLEDLMREKWLTAKAVYGFYPANRVGDDIE 1033
Query: 1013 IYRDETRTHVINVSHHLRQQTE-KTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDA 1071
+Y D++R+ V+ HHLRQQ++ K G AN CL+DFVAPK +G DYIG FAVT G+ +
Sbjct: 1034 VYTDDSRSEVLTRFHHLRQQSQKKRGGANNCLSDFVAPKDTGVKDYIGVFAVTTGIGIEE 1093
Query: 1072 LADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQ 1131
FEA HDDY IM+KALADR AEAFAE LH++VRK WGYAP+E L N+ LI E YQ
Sbjct: 1094 HIARFEAAHDDYRAIMLKALADRFAEAFAETLHQQVRKTDWGYAPDEALDNDALIAERYQ 1153
Query: 1132 GIRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYA 1191
GIRPA GYPACP+HTEK +W+LL+ ++ G+++TESFAM P A+VSG YF+HPDS+Y+
Sbjct: 1154 GIRPAAGYPACPDHTEKGLLWDLLKPDERIGLEITESFAMTPTAAVSGTYFAHPDSRYFG 1213
Query: 1192 VAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
V I RDQVEDYA+RK ++ + E+WLAPNLGYD +
Sbjct: 1214 VGSIGRDQVEDYAQRKDWTIEQAEKWLAPNLGYDPE 1249
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: 3796
Number of extensions: 159
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: 1253
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1205
Effective search space: 1420695
Effective search space used: 1420695
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_019894932.1 A377_RS0104280 (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.21704.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 1770.2 0.4 0 1770.0 0.4 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019894932.1 A377_RS0104280 methionine syntha
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384235.1:WP_019894932.1 A377_RS0104280 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1770.0 0.4 0 0 2 1182 .] 30 1214 .. 29 1214 .. 0.98
Alignments for each domain:
== domain 1 score: 1770.0 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+ ri+ lDGamGt++q+ +Lte +Frge ++d++++ +Gnnd+L +t+P++i++ihr++++aGaDiv
lcl|NCBI__GCF_000384235.1:WP_019894932.1 30 KTRIVRLDGAMGTMIQNLKLTESEFRGErFSDWSCDIQGNNDILAMTQPQLIENIHRQFLQAGADIV 96
6899*************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etn Fn+t+ia+adY++e+ + +ln +aa++ar+++d +t + +RfvaG+lGPtn++a++spdv+
lcl|NCBI__GCF_000384235.1:WP_019894932.1 97 ETNSFNATTIAQADYEMESIVTDLNIAAAEVARRACDALTDQDGEPRFVAGVLGPTNRTASISPDVN 163
****************************************9999*********************** PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p+ rn+t+d+lv+aY++++++l+ GG+D++Liet+fDtlnakaa+fav+++ +e g+e+Pi++sg+
lcl|NCBI__GCF_000384235.1:WP_019894932.1 164 DPGARNTTFDQLVEAYEQATRALITGGADVILIETIFDTLNAKAAIFAVKNIETELGDEIPIMLSGT 230
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d+sGrtLsGqt+eaf+++++ha+ l++GLnCalG++elr +v els+ ea+vs++PnaGLPn++
lcl|NCBI__GCF_000384235.1:WP_019894932.1 231 ITDASGRTLSGQTTEAFYNAVSHANPLSVGLNCALGPEELRRYVGELSRVCEAYVSIHPNAGLPNEF 297
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
geYd+ pe++a++++ +ae+g +ni+GGCCGttP+hi+a ++a+k+ +pr +e+ ++++lsgle+l
lcl|NCBI__GCF_000384235.1:WP_019894932.1 298 GEYDESPEQMAHEIAIWAEKGWINIIGGCCGTTPDHIAAFTQAMKNHTPRALPEIAPACRLSGLEPL 364
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+i+++s fvn+GeR nv+Gs+kf++li++++++ea++ia +qve+Gaq++D+n+De++lD++a m+k
lcl|NCBI__GCF_000384235.1:WP_019894932.1 365 NIDEDSLFVNVGERNNVTGSAKFKRLIIEDNFDEAIDIAVKQVEDGAQVIDVNMDEGMLDAKACMVK 431
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+llasepd ++vP+m+Dss++ev+eaGLk+iqGk+ivnsislk+Gee+F+++akl+++yGaa+++
lcl|NCBI__GCF_000384235.1:WP_019894932.1 432 FLNLLASEPDASRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISLKEGEEAFIKQAKLVRDYGAAAII 498
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t+++kiei++R y++l++kvgfpp+diifDpni+++atGieeh+ry++dfiea+r+i
lcl|NCBI__GCF_000384235.1:WP_019894932.1 499 MAFDEDGQADTYERKIEICERSYRVLVDKVGFPPQDIIFDPNIFAVATGIEEHNRYGLDFIEAVRWI 565
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
k++lP+akisgGvsnvsFs+rgn++vRea+hsvFLy+aik G+Dmgivnag++a+yd++++ lr++v
lcl|NCBI__GCF_000384235.1:WP_019894932.1 566 KQHLPHAKISGGVSNVSFSFRGNNPVREAIHSVFLYYAIKEGMDMGIVNAGQMAIYDEVPPKLRDAV 632
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed+il++++ea+e+Lle+ae y+g ++ s+ ++ wr+ +ve RL++al+kG++++ie+d+eea+
lcl|NCBI__GCF_000384235.1:WP_019894932.1 633 EDVILNKDPEASERLLEIAEEYRGDGTAASR-EADLTWREGDVESRLQHALIKGITDYIEDDTEEAY 698
***************************9776.66779****************************** PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGkiv 737
+kl ap+++iegpL+dGm++vGdLFG+GkmfLPqvvksarvmk+ava+L Pyl++ek+e + kGkiv
lcl|NCBI__GCF_000384235.1:WP_019894932.1 699 QKLGAPINVIEGPLMDGMNIVGDLFGAGKMFLPQVVKSARVMKRAVAHLDPYLQAEKAEGQVKGKIV 765
******************************************************************* PP
TIGR02082 738 latvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvev 804
latvkGDvhDiGkniv++vL+cn+++v+dlGv+vP e il+aa+k++a+v+glsGLi++sl+emv+v
lcl|NCBI__GCF_000384235.1:WP_019894932.1 766 LATVKGDVHDIGKNIVGIVLQCNNFDVIDLGVMVPGEDILDAAEKENANVVGLSGLITPSLEEMVNV 832
******************************************************************* PP
TIGR02082 805 aeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekik 871
a+ m++rg+++Pll+GGa++skah+avki+++Y+ +vvyvkdas+av v+++l+s++kka++++ki+
lcl|NCBI__GCF_000384235.1:WP_019894932.1 833 AKMMQERGMEVPLLIGGATTSKAHTAVKIEPQYEHPVVYVKDASRAVGVAQSLISHDKKAAFADKIR 899
******************************************************************* PP
TIGR02082 872 eeyeeirekfgekkeklialsekaarkevfaldrse....dlevpapkflGtkvleas.ieellkyi 933
+ey ++re + + ++++ +s+k+ar++ + + d ++++p flG++v+e+ +e+ll+
lcl|NCBI__GCF_000384235.1:WP_019894932.1 900 AEYADVREARKARAKEVKRVSIKQARQNPALKTLDDqawsDFTPTKPSFLGSRVIEDFpLETLLERF 966
**************************987655555555669************************** PP
TIGR02082 934 DwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddie 1000
Dw ++F +Wel+gkyp+il+d+++g+ea+k+f+dake+l+ l+ ek l+a++v+G++Pa++vgddie
lcl|NCBI__GCF_000384235.1:WP_019894932.1 967 DWSPFFQAWELHGKYPRILDDKVVGEEAKKVFADAKEMLEDLMREKWLTAKAVYGFYPANRVGDDIE 1033
******************************************************************* PP
TIGR02082 1001 iytdetvsqetkpiatvrekleqlrqqsdr.....ylclaDfiaskesGikDylgallvtaglgaee 1062
+ytd+++ +++ +++++lrqqs++ + cl+Df+a+k++G kDy+g+++vt+g+g+ee
lcl|NCBI__GCF_000384235.1:WP_019894932.1 1034 VYTDDSR---SEVL----TRFHHLRQQSQKkrggaNNCLSDFVAPKDTGVKDYIGVFAVTTGIGIEE 1093
***9998...3333....34555555555555557******************************** PP
TIGR02082 1063 lakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafG 1129
++ea +ddy +i++kaladr+aea+ae+lh++vRk wgya +e+ld++ l+ erY+Girpa G
lcl|NCBI__GCF_000384235.1:WP_019894932.1 1094 HIARFEAAHDDYRAIMLKALADRFAEAFAETLHQQVRKTDWGYAPDEALDNDALIAERYQGIRPAAG 1160
******************************************************************* PP
TIGR02082 1130 YpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
YpacPdhtek l++Ll++++ iGl++tes+a++P+a+vsg yfahp+++Yf v
lcl|NCBI__GCF_000384235.1:WP_019894932.1 1161 YPACPDHTEKGLLWDLLKPDErIGLEITESFAMTPTAAVSGTYFAHPDSRYFGV 1214
******************9777******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1253 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 0.04s 00:00:00.12 Elapsed: 00:00:00.11
# Mc/sec: 12.63
//
[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