Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_028487376.1 B076_RS0111075 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000483485.1:WP_028487376.1
Length = 1236
Score = 1597 bits (4136), Expect = 0.0
Identities = 797/1230 (64%), Positives = 974/1230 (79%), Gaps = 6/1230 (0%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
+ ++EQL++ L ERI+VLDG MGTMIQ L+E DFRGERFAD+ D+KGNND+LV+++P
Sbjct: 5 TQRLEQLKSLLQERIMVLDGAMGTMIQDKNLSEEDFRGERFADYHMDIKGNNDILVITQP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
++I IH + G DI+ETN+FN+TTIA ADY M+ +EIN AAAK+AR D A
Sbjct: 65 DIIRDIHLDFLRNGVDILETNSFNATTIAQADYDMQEYVSEINLAAAKVAREACDIAQAE 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
KPR+V GVLGPTNRTASISPDVNDP +RN +FD LV AY+++T AL+EGG D ILIE
Sbjct: 125 DG-KPRFVTGVLGPTNRTASISPDVNDPGYRNTSFDELVTAYKQATHALLEGGVDAILIE 183
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FAVK + +G E+PIM+SGTITDASGRTLSGQTTEAFYN++ HAE L
Sbjct: 184 TIFDTLNAKAAIFAVKEVEDEVGYEVPIMLSGTITDASGRTLSGQTTEAFYNAVAHAEPL 243
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALGP+ELR YV+ELSR+ E +V+ HPNAGLPN FGEYD + MAK+I+ WA+
Sbjct: 244 SVGLNCALGPEELRPYVEELSRVCETFVSVHPNAGLPNEFGEYDESPEQMAKEIKIWAER 303
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
G++NI+GGCCGTTP H+ AM+ A + R++P++ ACRLSGLEPLNI E SLFVNVGE
Sbjct: 304 GWINIIGGCCGTTPDHVKAMAEAAQAFPRREIPQVKPACRLSGLEPLNIDESSLFVNVGE 363
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
R NVTGSAKFKRLI EE Y EA+++A +QVE+GAQIID+NMDEGMLDA+A MVRFLNL+A
Sbjct: 364 RNNVTGSAKFKRLIIEENYDEAIEIAVKQVEDGAQIIDVNMDEGMLDAKACMVRFLNLLA 423
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
EP+ +RVPIMIDSSKW+VIE GLKCIQGKG+VNSIS+KEG +AFI HAKL+++YGAA +
Sbjct: 424 SEPEASRVPIMIDSSKWEVIEAGLKCIQGKGVVNSISLKEGEEAFIQHAKLVKKYGAAAI 483
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
+MAFDE GQADT RKIEIC R+Y++L ++VGF P+DIIFDPNIFAVATGIEEHNNY D
Sbjct: 484 IMAFDEDGQADTLERKIEICERSYRVLVDKVGFLPQDIIFDPNIFAVATGIEEHNNYGLD 543
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI A IK LPHA ISGGVSNVSFSFRGN+PVREAIH+VFLYYAI+ GMDMGIVNAGQ
Sbjct: 544 FINAVTWIKANLPHAKISGGVSNVSFSFRGNNPVREAIHSVFLYYAIKEGMDMGIVNAGQ 603
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
+AIYDDLP +LR AVEDVI+N + ERLLE+AE++RG T T+ WR EV K
Sbjct: 604 MAIYDDLPEKLRLAVEDVIMNTDPEAGERLLEVAEEFRGDGT-ATSKVADTAWREAEVEK 662
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LVKGIT++IE DTEEA Q++ ++VIEG LMDGMNVVGDLFG GKMFLPQVVKS
Sbjct: 663 RLEHALVKGITDYIEADTEEAYQKSGSALQVIEGSLMDGMNVVGDLFGSGKMFLPQVVKS 722
Query: 722 ARVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLG 781
ARVMK+AVAYL+P++ A K +G+ NGK+V+ATVKGDVHDIGKNIVGVVLQCNN+E++DLG
Sbjct: 723 ARVMKRAVAYLDPYLLAQKAEGQANGKIVMATVKGDVHDIGKNIVGVVLQCNNFEVIDLG 782
Query: 782 VMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAH 841
VMVPAEKIL TA E A++IGLSGLITPSL+EMVNVAK M+ + +PLLIGGATTSKAH
Sbjct: 783 VMVPAEKILDTAVEQGANVIGLSGLITPSLEEMVNVAKLMKERNMDLPLLIGGATTSKAH 842
Query: 842 TAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRT 901
TAVKIE Y P VYV++ASR VGV +L+S+ + D+ A+ R EYE VR + + +
Sbjct: 843 TAVKIEPQYDHPVVYVKDASRAVGVAQSLISNDLKVDYAAKIRAEYEQVREERKARAAQV 902
Query: 902 PPVTLEAARDNDFAFD--WQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAG 958
+ + AR+N + W Y P LG + + + +E L DW+PFF +W L G
Sbjct: 903 KRIPINKARENPALNEQAWSDYMPVKPTFLGSKVLNDFPLEKLVERFDWSPFFQSWELHG 962
Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDET 1018
YPRIL+D+VVG EA+++F DA +ML ++ EK L + V G +PANRVGDDIE+Y DE+
Sbjct: 963 LYPRILDDKVVGEEARKVFADAKEMLQQIVDEKWLTAKAVYGFYPANRVGDDIEVYADES 1022
Query: 1019 RTHVINVSHHLRQQTE-KTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFE 1077
RT VI+ HHLRQQ E K G AN CL+DF+A K SG ADYIG FAVT G+ D + FE
Sbjct: 1023 RTQVIHKFHHLRQQAEKKRGGANNCLSDFIASKDSGVADYIGFFAVTAGIGIDEHIERFE 1082
Query: 1078 AQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAP 1137
+HDDY IM+KALADR AEAFAE LHE VRK WGYAP+E L NE+LIRE YQGIRPA
Sbjct: 1083 KEHDDYRSIMLKALADRFAEAFAETLHEIVRKEDWGYAPDEQLENEDLIRERYQGIRPAA 1142
Query: 1138 GYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQR 1197
GYPACP+HTEK +WELL+ ++ G+++TESFAM P A+VSG YF+HPDS+Y+ V + R
Sbjct: 1143 GYPACPDHTEKGILWELLKPDQEIGLEITESFAMTPTAAVSGTYFAHPDSRYFGVGSLGR 1202
Query: 1198 DQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
DQVEDYARRKG S+ + E+WLAPNLGYD +
Sbjct: 1203 DQVEDYARRKGWSIEKAEQWLAPNLGYDPE 1232
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: 3751
Number of extensions: 145
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: 1236
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1189
Effective search space: 1403020
Effective search space used: 1403020
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_028487376.1 B076_RS0111075 (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.26052.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 1767.7 3.6 0 1767.5 3.6 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028487376.1 B076_RS0111075 methionine syntha
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000483485.1:WP_028487376.1 B076_RS0111075 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1767.5 3.6 0 0 1 1182 [] 15 1197 .. 15 1197 .. 0.98
Alignments for each domain:
== domain 1 score: 1767.5 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++ri+vlDGamGt++q +nL e+dFrge +ad++++ kGnnd+L++t+P++i++ih +++ G Di
lcl|NCBI__GCF_000483485.1:WP_028487376.1 15 LQERIMVLDGAMGTMIQDKNLSEEDFRGErFADYHMDIKGNNDILVITQPDIIRDIHLDFLRNGVDI 81
689**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdv 133
+etn Fn+t+ia+adYd+++ + e+n +aak+are++d + + k+Rfv G+lGPtn++a++spdv
lcl|NCBI__GCF_000483485.1:WP_028487376.1 82 LETNSFNATTIAQADYDMQEYVSEINLAAAKVAREACDIAQAEDGKPRFVTGVLGPTNRTASISPDV 148
******************************************************************* PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p++rn+ +delv aYk+++++ll+GGvD++Liet+fDtlnakaa+fav+ev +e g e+Pi++sg
lcl|NCBI__GCF_000483485.1:WP_028487376.1 149 NDPGYRNTSFDELVTAYKQATHALLEGGVDAILIETIFDTLNAKAAIFAVKEVEDEVGYEVPIMLSG 215
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267
+i+d+sGrtLsGqt+eaf++++ hae l++GLnCalG++elr++v+els+ e++vsv+PnaGLPn+
lcl|NCBI__GCF_000483485.1:WP_028487376.1 216 TITDASGRTLSGQTTEAFYNAVAHAEPLSVGLNCALGPEELRPYVEELSRVCETFVSVHPNAGLPNE 282
******************************************************************* PP
TIGR02082 268 lgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglea 334
+geYd+ pe++ak++k +ae g +ni+GGCCGttP+h++a+aea++ +r+ ++++++++lsgle+
lcl|NCBI__GCF_000483485.1:WP_028487376.1 283 FGEYDESPEQMAKEIKIWAERGWINIIGGCCGTTPDHVKAMAEAAQAFPRREIPQVKPACRLSGLEP 349
******************************************************************* PP
TIGR02082 335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401
l+i++ s fvn+GeR nv+Gs+kf++li++e+y+ea++ia +qve+Gaqi+D+n+De++lD++a m+
lcl|NCBI__GCF_000483485.1:WP_028487376.1 350 LNIDESSLFVNVGERNNVTGSAKFKRLIIEENYDEAIEIAVKQVEDGAQIIDVNMDEGMLDAKACMV 416
******************************************************************* PP
TIGR02082 402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468
++l+llasep+ ++vP+m+Dss++ev+eaGLk+iqGk++vnsislk+Gee+F+++akl+k+yGaa++
lcl|NCBI__GCF_000483485.1:WP_028487376.1 417 RFLNLLASEPEASRVPIMIDSSKWEVIEAGLKCIQGKGVVNSISLKEGEEAFIQHAKLVKKYGAAAI 483
******************************************************************* PP
TIGR02082 469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535
+mafDe+Gqa+t ++kiei++R y++l++kvgf p+diifDpni+++atGieeh++y++dfi+a+ +
lcl|NCBI__GCF_000483485.1:WP_028487376.1 484 IMAFDEDGQADTLERKIEICERSYRVLVDKVGFLPQDIIFDPNIFAVATGIEEHNNYGLDFINAVTW 550
******************************************************************* PP
TIGR02082 536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602
ik +lP+akisgGvsnvsFs+rgn++vRea+hsvFLy+aik G+Dmgivnag++a+ydd+++ lr +
lcl|NCBI__GCF_000483485.1:WP_028487376.1 551 IKANLPHAKISGGVSNVSFSFRGNNPVREAIHSVFLYYAIKEGMDMGIVNAGQMAIYDDLPEKLRLA 617
******************************************************************* PP
TIGR02082 603 vedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleea 669
ved+i++ ++ea e+Lle+ae ++g +++sk + +wr+ +ve+RLe+alvkG++++ie+d+eea
lcl|NCBI__GCF_000483485.1:WP_028487376.1 618 VEDVIMNTDPEAGERLLEVAEEFRGDGTATSK-VADTAWREAEVEKRLEHALVKGITDYIEADTEEA 683
*****************************777.77889***************************** PP
TIGR02082 670 rkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGki 736
++k ++l++ieg L+dGm+vvGdLFGsGkmfLPqvvksarvmk+avayL Pyl ++k+e +++Gki
lcl|NCBI__GCF_000483485.1:WP_028487376.1 684 YQKSGSALQVIEGSLMDGMNVVGDLFGSGKMFLPQVVKSARVMKRAVAYLDPYLLAQKAEGQANGKI 750
******************************************************************* PP
TIGR02082 737 vlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemve 803
v+atvkGDvhDiGkniv+vvL+cn++ev+dlGv+vP+ekil++a ++ a+viglsGLi++sl+emv+
lcl|NCBI__GCF_000483485.1:WP_028487376.1 751 VMATVKGDVHDIGKNIVGVVLQCNNFEVIDLGVMVPAEKILDTAVEQGANVIGLSGLITPSLEEMVN 817
******************************************************************* PP
TIGR02082 804 vaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeeleki 870
va+ m++r++++Pll+GGa++skah+avki+++Y+ +vvyvkdas+av v+++l+s++ k ++++ki
lcl|NCBI__GCF_000483485.1:WP_028487376.1 818 VAKLMKERNMDLPLLIGGATTSKAHTAVKIEPQYDHPVVYVKDASRAVGVAQSLISNDLKVDYAAKI 884
******************************************************************* PP
TIGR02082 871 keeyeeirekfgekkeklialsekaarkevf..aldrsedlevpapkflGtkvleas.ieellkyiD 934
++eye++re+ + + +++ +++++ar++ + +s d+ +++p+flG+kvl++ +e+l++ D
lcl|NCBI__GCF_000483485.1:WP_028487376.1 885 RAEYEQVREERKARAAQVKRIPINKARENPAlnEQAWS-DYMPVKPTFLGSKVLNDFpLEKLVERFD 950
*********99999999999998888877541144566.**************************** PP
TIGR02082 935 wkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddiei 1001
w ++F +Wel+g yp+il+d+++g+eark+f+dake+l++++ ek l+a++v+G++Pa++vgddie+
lcl|NCBI__GCF_000483485.1:WP_028487376.1 951 WSPFFQSWELHGLYPRILDDKVVGEEARKVFADAKEMLQQIVDEKWLTAKAVYGFYPANRVGDDIEV 1017
******************************************************************* PP
TIGR02082 1002 ytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkl 1067
y+de+++q +++ + ++q++++++ + cl+Dfiask+sG +Dy+g+++vtag+g++e +++
lcl|NCBI__GCF_000483485.1:WP_028487376.1 1018 YADESRTQVIHKFHHL---RQQAEKKRGGaNNCLSDFIASKDSGVADYIGFFAVTAGIGIDEHIERF 1081
****995555555444...455555555459************************************ PP
TIGR02082 1068 eakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacP 1134
e+++ddy si++kaladr+aea+ae+lhe vRke wgya +e+l++edl++erY+Girpa GYpacP
lcl|NCBI__GCF_000483485.1:WP_028487376.1 1082 EKEHDDYRSIMLKALADRFAEAFAETLHEIVRKEDWGYAPDEQLENEDLIRERYQGIRPAAGYPACP 1148
******************************************************************* PP
TIGR02082 1135 dhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
dhtek l+eLl++++ iGl++tes+a++P+a+vsg yfahp+++Yf v
lcl|NCBI__GCF_000483485.1:WP_028487376.1 1149 DHTEKGILWELLKPDQeIGLEITESFAMTPTAAVSGTYFAHPDSRYFGV 1197
***********************************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1236 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 0.03s 00:00:00.12 Elapsed: 00:00:00.11
# Mc/sec: 13.06
//
[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