Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_074201854.1 BUQ81_RS07800 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_900141795.1:WP_074201854.1
Length = 1234
Score = 1608 bits (4165), Expect = 0.0
Identities = 792/1228 (64%), Positives = 977/1228 (79%), Gaps = 6/1228 (0%)
Query: 3 SKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPE 62
++++QL+ L +R++VLDG MGTMIQ L+E DFRGERFADW D+KGNND+L +++P+
Sbjct: 6 TRIQQLKDLLKQRVVVLDGAMGTMIQGLNLSEEDFRGERFADWHMDIKGNNDILCMTQPQ 65
Query: 63 VIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTART 122
+I IH + G DIIETN+FN+TTIA ADY ME + E+N AAAK+AR AD+ A
Sbjct: 66 LIKDIHLQFLRRGVDIIETNSFNATTIAQADYDMEGIVTELNIAAAKVAREAADQAQAED 125
Query: 123 PEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIET 182
KPR+VAGVLGPTNRTASISPDVNDP +RN+T+D LVAAY E+ + L+EGGAD+ILIET
Sbjct: 126 G-KPRFVAGVLGPTNRTASISPDVNDPGYRNVTYDELVAAYDEAVRGLIEGGADVILIET 184
Query: 183 VFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALT 242
+FDTLNAKAA+FAVK +ALG ELPIM+SGTITDASGRTLSGQTTEAFYNS+RHAE L+
Sbjct: 185 IFDTLNAKAAIFAVKQYEKALGEELPIMLSGTITDASGRTLSGQTTEAFYNSVRHAEPLS 244
Query: 243 FGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAG 302
GLNCALGP+ELR YV+ L+++ E YV+ HPNAGLPN FGEYD MA +++ WA+ G
Sbjct: 245 IGLNCALGPEELRPYVETLAKVCETYVSVHPNAGLPNEFGEYDETPQQMAAEVKHWAEQG 304
Query: 303 FLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGER 362
++NI+GGCCGTTP H+AAM+ PRKLP +PV RL+GLEPLNIG+DSLFVNVGER
Sbjct: 305 WVNIIGGCCGTTPDHVAAMAEVCLAHPPRKLPTLPVETRLAGLEPLNIGDDSLFVNVGER 364
Query: 363 TNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAG 422
NVTGSA+FKRLI EE Y EA+++A +QV +GAQIID+NMDEGMLD +AAMVRFLNL+AG
Sbjct: 365 NNVTGSARFKRLILEENYEEAIEIAIRQVHDGAQIIDVNMDEGMLDGKAAMVRFLNLLAG 424
Query: 423 EPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVV 482
EP+ ARVP+MIDSSKW+V+E G+KC+QGKGI+NSIS+KEG + F+ AK +R YG A +V
Sbjct: 425 EPEAARVPVMIDSSKWEVLEAGMKCVQGKGIINSISLKEGEEKFLEQAKKIREYGFAAIV 484
Query: 483 MAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDF 542
MAFDE+GQADT RKIEIC+R+Y +L GFPPEDIIFDPNIFAVATGIEEH+NYA DF
Sbjct: 485 MAFDEEGQADTFERKIEICKRSYDLLVAN-GFPPEDIIFDPNIFAVATGIEEHDNYAVDF 543
Query: 543 IGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQL 602
I A IK+ LPHA +SGGVSNVSFSFRGN+PVREAIHAVFLY+AI+ GMDMGIVNAGQL
Sbjct: 544 IEAVRWIKQNLPHAKVSGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQL 603
Query: 603 AIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKR 662
A+YD++P ELR+AVEDVILNR +E+LLE+AEKYRG + + Q EWR+ V KR
Sbjct: 604 AVYDEIPEELRNAVEDVILNRYAGASEKLLEIAEKYRGDGSVQ-SKEQDTEWRNAPVEKR 662
Query: 663 LEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA 722
LE++LVKGI ++I++DT EA ++ P++VIEGPLMDGMNVVGDLFG GKMFLPQVVKSA
Sbjct: 663 LEHALVKGIIDYIDEDTAEALEKLKSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSA 722
Query: 723 RVMKQAVAYLEPFIEASKEQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGV 782
RVMK+AVA+L+P++EA K GK+++ATVKGDVHDIGKNIV VVLQCN +E++DLGV
Sbjct: 723 RVMKKAVAWLQPYLEAEKVGSSAQGKIIMATVKGDVHDIGKNIVAVVLQCNGFEVIDLGV 782
Query: 783 MVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHT 842
MVPAE IL+ A+E NAD+IGLSGLITPSLDEMVNVAKEM+RQGFT+PLLIGGATTSKAHT
Sbjct: 783 MVPAETILKAAQEHNADIIGLSGLITPSLDEMVNVAKEMKRQGFTLPLLIGGATTSKAHT 842
Query: 843 AVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTP 902
AVKIE Y VYV++ASR VGV L+SD + F+ RKEYE +RI+ + +T
Sbjct: 843 AVKIEPEYPHGVVYVKDASRAVGVAQNLISDELKGPFLEEVRKEYEQIRIERKARAQQTR 902
Query: 903 PVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAGKYP 961
V ++ AR+N W YTPP + LG++ + +E L DW+PFF W L G +P
Sbjct: 903 RVPIKKARENRVPIQWDGYTPPRPNLLGIKVFDHYDLEELLERFDWSPFFQAWELHGLFP 962
Query: 962 RILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVG-DDIEIYRDETRT 1020
RIL+D+VVG +A++++ DA M+ ++ E+ L R V+G +PAN V DDIE+Y D++R+
Sbjct: 963 RILDDKVVGEQARKVYSDAQKMVRQIIDEQWLEARAVIGFWPANTVNDDDIELYSDDSRS 1022
Query: 1021 HVINVSHHLRQQTEKTGFA-NYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQ 1079
V+ H LRQQ EK A NYCL+D+VAPK SG ADY+G FAVT G+ D FEA
Sbjct: 1023 EVLTTLHMLRQQMEKRADAPNYCLSDYVAPKESGLADYVGLFAVTAGIGIDEHLARFEAA 1082
Query: 1080 HDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGY 1139
DDYN IM+KALADR AEAFAE +HERVRK +WGYAP+ENLSNEE+I+E Y+GIRPAPGY
Sbjct: 1083 GDDYNSIMLKALADRFAEAFAERMHERVRKEFWGYAPDENLSNEEIIKEKYRGIRPAPGY 1142
Query: 1140 PACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQ 1199
PACP+HTEK T+W+LL+ + + LTES+AM P A+VSG+YFSHP S+Y+ V I RDQ
Sbjct: 1143 PACPDHTEKGTLWQLLQPDARIDLHLTESYAMTPTAAVSGYYFSHPQSRYFGVGAIGRDQ 1202
Query: 1200 VEDYARRKGMSVTEVERWLAPNLGYDAD 1227
VEDYARRKG ++ E E+WLAPNLGYD +
Sbjct: 1203 VEDYARRKGWTIDEAEKWLAPNLGYDPE 1230
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: 3812
Number of extensions: 143
Number of successful extensions: 7
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: 1234
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1187
Effective search space: 1400660
Effective search space used: 1400660
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_074201854.1 BUQ81_RS07800 (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.20360.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 1787.8 0.0 0 1787.6 0.0 1.0 1 lcl|NCBI__GCF_900141795.1:WP_074201854.1 BUQ81_RS07800 methionine synthas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900141795.1:WP_074201854.1 BUQ81_RS07800 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1787.6 0.0 0 0 1 1182 [] 15 1195 .. 15 1195 .. 0.99
Alignments for each domain:
== domain 1 score: 1787.6 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDi 66
l++r++vlDGamGt++q nL e+dFrge +ad++++ kGnnd+L +t+P++i++ih +++ G Di
lcl|NCBI__GCF_900141795.1:WP_074201854.1 15 LKQRVVVLDGAMGTMIQGLNLSEEDFRGErFADWHMDIKGNNDILCMTQPQLIKDIHLQFLRRGVDI 81
589**************************************************************** PP
TIGR02082 67 vetntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdv 133
+etn Fn+t+ia+adYd+e + eln +aak+are+ad+ + + k+RfvaG+lGPtn++a++spdv
lcl|NCBI__GCF_900141795.1:WP_074201854.1 82 IETNSFNATTIAQADYDMEGIVTELNIAAAKVAREAADQAQAEDGKPRFVAGVLGPTNRTASISPDV 148
******************************************************************* PP
TIGR02082 134 erpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisg 200
++p++rnvtydelv+aY e+v+gl++GG+D++Liet+fDtlnakaa+fav++ ++ g+elPi++sg
lcl|NCBI__GCF_900141795.1:WP_074201854.1 149 NDPGYRNVTYDELVAAYDEAVRGLIEGGADVILIETIFDTLNAKAAIFAVKQYEKALGEELPIMLSG 215
******************************************************************* PP
TIGR02082 201 vivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPna 267
+i+d+sGrtLsGqt+eaf++s++hae l++GLnCalG++elr++v++l++ e++vsv+PnaGLPn+
lcl|NCBI__GCF_900141795.1:WP_074201854.1 216 TITDASGRTLSGQTTEAFYNSVRHAEPLSIGLNCALGPEELRPYVETLAKVCETYVSVHPNAGLPNE 282
******************************************************************* PP
TIGR02082 268 lgeYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglea 334
+geYd+tp+++a+++k++ae+g +ni+GGCCGttP+h++a+ae+ prk ++l+ +++l+gle+
lcl|NCBI__GCF_900141795.1:WP_074201854.1 283 FGEYDETPQQMAAEVKHWAEQGWVNIIGGCCGTTPDHVAAMAEVCLAHPPRKLPTLPVETRLAGLEP 349
******************************************************************* PP
TIGR02082 335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401
l+i+++s fvn+GeR nv+Gs++f++li +e+yeea++ia +qv++Gaqi+D+n+De++lDg+a+m+
lcl|NCBI__GCF_900141795.1:WP_074201854.1 350 LNIGDDSLFVNVGERNNVTGSARFKRLILEENYEEAIEIAIRQVHDGAQIIDVNMDEGMLDGKAAMV 416
******************************************************************* PP
TIGR02082 402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468
++l+lla+ep+ a+vP+m+Dss++evleaG+k++qGk+i+nsislk+Gee+Fle+ak+i+eyG a++
lcl|NCBI__GCF_900141795.1:WP_074201854.1 417 RFLNLLAGEPEAARVPVMIDSSKWEVLEAGMKCVQGKGIINSISLKEGEEKFLEQAKKIREYGFAAI 483
******************************************************************* PP
TIGR02082 469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535
vmafDeeGqa+t ++kiei+kR y+ll++ gfppediifDpni+++atGieehd+ya+dfiea+r+
lcl|NCBI__GCF_900141795.1:WP_074201854.1 484 VMAFDEEGQADTFERKIEICKRSYDLLVA-NGFPPEDIIFDPNIFAVATGIEEHDNYAVDFIEAVRW 549
****************************9.8************************************ PP
TIGR02082 536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602
ik++lP+ak+sgGvsnvsFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+lavyd+i++elr++
lcl|NCBI__GCF_900141795.1:WP_074201854.1 550 IKQNLPHAKVSGGVSNVSFSFRGNNPVREAIHAVFLYHAIQAGMDMGIVNAGQLAVYDEIPEELRNA 616
******************************************************************* PP
TIGR02082 603 vedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleea 669
ved+il+r a+ekLle+ae+y+g + +sk +q ewrn pve+RLe+alvkG+ ++i+ed+ ea
lcl|NCBI__GCF_900141795.1:WP_074201854.1 617 VEDVILNRYAGASEKLLEIAEKYRGDGSVQSK-EQDTEWRNAPVEKRLEHALVKGIIDYIDEDTAEA 682
***************************99777.8899****************************** PP
TIGR02082 670 rkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeedkskGki 736
++klk+pl++iegpL+dGm+vvGdLFG+GkmfLPqvvksarvmkkava+L+Pyle+ek ++++Gki
lcl|NCBI__GCF_900141795.1:WP_074201854.1 683 LEKLKSPLQVIEGPLMDGMNVVGDLFGAGKMFLPQVVKSARVMKKAVAWLQPYLEAEKVGSSAQGKI 749
******************************************************************* PP
TIGR02082 737 vlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemve 803
++atvkGDvhDiGkniv vvL+cng+ev+dlGv+vP+e+il+aa++++aD+iglsGLi++sldemv+
lcl|NCBI__GCF_900141795.1:WP_074201854.1 750 IMATVKGDVHDIGKNIVAVVLQCNGFEVIDLGVMVPAETILKAAQEHNADIIGLSGLITPSLDEMVN 816
******************************************************************* PP
TIGR02082 804 vaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeeleki 870
va+em+r+g+++Pll+GGa++skah+avki+++Y vvyvkdas+av v+++l+s++ k ++le++
lcl|NCBI__GCF_900141795.1:WP_074201854.1 817 VAKEMKRQGFTLPLLIGGATTSKAHTAVKIEPEYPHGVVYVKDASRAVGVAQNLISDELKGPFLEEV 883
******************************************************************* PP
TIGR02082 871 keeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwk 936
++eye+ir + + + ++++ +++k+ar++++ +++ +++p p+ lG+kv++++ +eell+ Dw
lcl|NCBI__GCF_900141795.1:WP_074201854.1 884 RKEYEQIRIERKARAQQTRRVPIKKARENRVPIQWD-GYTPPRPNLLGIKVFDHYdLEELLERFDWS 949
***********************************9.9***************************** PP
TIGR02082 937 alFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvg.ddieiy 1002
++F +Wel+g +p+il+d+++g++ark+++da++++ +++ e+ l+ar+v+G++Pa++v+ ddie+y
lcl|NCBI__GCF_900141795.1:WP_074201854.1 950 PFFQAWELHGLFPRILDDKVVGEQARKVYSDAQKMVRQIIDEQWLEARAVIGFWPANTVNdDDIELY 1016
*********************************************************876268**** PP
TIGR02082 1003 tdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkle 1068
+d+++ ++++t++ ++q+++ d ++cl+D++a+kesG +Dy+g+++vtag+g++e ++e
lcl|NCBI__GCF_900141795.1:WP_074201854.1 1017 SDDSR---SEVLTTLHMLRQQMEKRADApNYCLSDYVAPKESGLADYVGLFAVTAGIGIDEHLARFE 1080
*9999...677777777778888888778************************************** PP
TIGR02082 1069 akeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPd 1135
a ddy+si++kaladr+aea+ae +hervRke+wgya +enl++e+++ke+YrGirpa+GYpacPd
lcl|NCBI__GCF_900141795.1:WP_074201854.1 1081 AAGDDYNSIMLKALADRFAEAFAERMHERVRKEFWGYAPDENLSNEEIIKEKYRGIRPAPGYPACPD 1147
******************************************************************* PP
TIGR02082 1136 htekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
htek tl++Ll+++ i l+ltes+a++P+a+vsg+yf+hp+++Yf v
lcl|NCBI__GCF_900141795.1:WP_074201854.1 1148 HTEKGTLWQLLQPDArIDLHLTESYAMTPTAAVSGYYFSHPQSRYFGV 1195
*************988******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1234 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: 0.10u 0.05s 00:00:00.15 Elapsed: 00:00:00.14
# Mc/sec: 9.82
//
[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