Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012384122.1 BIND_RS05695 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000019845.1:WP_012384122.1
Length = 1246
Score = 1516 bits (3925), Expect = 0.0
Identities = 772/1220 (63%), Positives = 931/1220 (76%), Gaps = 11/1220 (0%)
Query: 14 ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73
ER+LVLDG MGTMIQ + EADFRGERF DWP DL+GNNDLL L++P+ I AIH AYFE
Sbjct: 21 ERVLVLDGAMGTMIQQRKFTEADFRGERFKDWPSDLRGNNDLLTLTQPDAIVAIHRAYFE 80
Query: 74 AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133
AGADII TNTFNST I+ ADY ME L AE+N +A+LAR ADE A+ + R+VAG L
Sbjct: 81 AGADIIGTNTFNSTRISQADYGMEELVAELNRESARLARQAADEAEAKDGRR-RFVAGAL 139
Query: 134 GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193
GPTNRTASISPDVN+P FR +TFD L AAY E+ AL+EGGAD++++ET+FDTLNAKAA+
Sbjct: 140 GPTNRTASISPDVNNPGFRAVTFDDLRAAYAEAASALIEGGADILIVETIFDTLNAKAAL 199
Query: 194 FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253
A+ +E+L V LP+MISGTITD SGRTLSGQT AF+ SLRH + +T GLNCALG E
Sbjct: 200 AAIDDVYESLNVRLPVMISGTITDLSGRTLSGQTPTAFWYSLRHVKPITIGLNCALGARE 259
Query: 254 LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313
+R ++ ELSR+A+ + A+PNAGLPN FG YD + MA + E+A+AG +NIVGGCCGT
Sbjct: 260 MRAHIAELSRVADTLICAYPNAGLPNEFGLYDESPEYMASLVGEFAEAGLVNIVGGCCGT 319
Query: 314 TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373
TP HI A+++ V G+APRK+P I RLSGLEP + +D FVNVGERTNVTGSAKF++
Sbjct: 320 TPAHIHAIAKRVAGIAPRKIPAIEPLLRLSGLEPFTLTKDIRFVNVGERTNVTGSAKFRK 379
Query: 374 LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433
LIKE ++S ALDVAR QV GAQ+ID+NMDEG+LD+EA M FLNL+A EPDIARVP+MI
Sbjct: 380 LIKEGQFSAALDVARDQVVMGAQVIDVNMDEGLLDSEAVMRDFLNLVAAEPDIARVPVMI 439
Query: 434 DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493
DSSK+ VIE GLKCIQGKGIVNSIS+KEG + FI AK + RYGAAVVVMAFDEQGQADT
Sbjct: 440 DSSKFVVIEAGLKCIQGKGIVNSISLKEGEENFIQAAKAVHRYGAAVVVMAFDEQGQADT 499
Query: 494 RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553
RARK+EIC RAY IL GFPPEDIIFDPNIFAVATGIEEHNNY DFI A +I+++
Sbjct: 500 RARKVEICSRAYDILVNRCGFPPEDIIFDPNIFAVATGIEEHNNYGVDFIEATREIRQKF 559
Query: 554 PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613
P ISGGVSN+SFSFRGN+PVR+A+H+VFLY+AI GMDMGIVNAGQL++Y++L ELR
Sbjct: 560 PLVHISGGVSNLSFSFRGNEPVRQAMHSVFLYHAIAAGMDMGIVNAGQLSVYEELDPELR 619
Query: 614 DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673
+A EDV+LNRR + TERLL LAE Y+G T+ + WR V KRLE++LV GITE
Sbjct: 620 EACEDVVLNRRPEATERLLALAENYKGQGTE--KQEKSLAWREEPVEKRLEHALVNGITE 677
Query: 674 FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733
FI+QD EEAR +TR ++VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMK AVAYL
Sbjct: 678 FIDQDVEEARLASTRTLDVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMKAAVAYLM 737
Query: 734 PFIEASKEQG-----KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEK 788
PF+EA K + GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGVMVPA K
Sbjct: 738 PFMEAEKAANGGAVRSSAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAK 797
Query: 789 ILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIEQ 848
IL TA+ D IGLSGLITPSLDEM VA E+ER+GF +PLLIGGATTS+ HTAVKI
Sbjct: 798 ILETARAEQVDCIGLSGLITPSLDEMCFVAAELEREGFDVPLLIGGATTSRVHTAVKIHP 857
Query: 849 NYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTLE 907
NY+ G TVYV +ASR VG V +LLS+T R ++ R EY+ V H R + + L+
Sbjct: 858 NYTRGQTVYVTDASRAVGTVQSLLSETSRGAYIETIRAEYQKVSDAHRRAEAEKQRLPLQ 917
Query: 908 AARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPRILED 966
AR N F DW AY PP G + + + L YIDWTPFF TW L G+YP +L+D
Sbjct: 918 RARQNAFRPDWAAYQPPRPTFTGARIFGSYDVGELVPYIDWTPFFQTWELRGRYPALLDD 977
Query: 967 EVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVS 1026
G A++LF DA ML ++ E +P+ V+G +PAN V DDI++Y E+R+ +
Sbjct: 978 PKQGASARQLFDDAQAMLKRIVEEHWFDPKAVIGFWPANAVDDDIKLYTGESRSEELATF 1037
Query: 1027 HHLRQQTEKTG-FANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYNK 1085
LRQQ K G N LADFVAP+ SGKADYIG F VT G E+ +A+ F +DDY
Sbjct: 1038 FTLRQQLSKQGDKPNLALADFVAPRDSGKADYIGGFVVTAGAREEKIAERFAKANDDYGS 1097
Query: 1086 IMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPEH 1145
IMVKALADR+AEAFAE +HERVR+ +W YAP+ENL+NEE I E+Y+GIRPAPGYPA P+H
Sbjct: 1098 IMVKALADRIAEAFAERMHERVRREFWAYAPDENLTNEERISESYRGIRPAPGYPAQPDH 1157
Query: 1146 TEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYAR 1205
+EKAT++ LLE E+ + LTESFAMWPG+SVSG Y + P++ Y+ VA+++RDQVEDYAR
Sbjct: 1158 SEKATLFRLLEAERRISVSLTESFAMWPGSSVSGLYIAQPEAYYFGVAKVERDQVEDYAR 1217
Query: 1206 RKGMSVTEVERWLAPNLGYD 1225
RKGMS+ EVERWL P L Y+
Sbjct: 1218 RKGMSIAEVERWLTPILNYN 1237
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: 3635
Number of extensions: 141
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: 1246
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1198
Effective search space: 1412442
Effective search space used: 1412442
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_012384122.1 BIND_RS05695 (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.11592.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 1767.9 0.0 0 1767.7 0.0 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012384122.1 BIND_RS05695 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012384122.1 BIND_RS05695 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1767.7 0.0 0 0 2 1182 .] 20 1204 .. 19 1204 .. 0.99
Alignments for each domain:
== domain 1 score: 1767.7 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+r+lvlDGamGt++q+ + teadFrge ++d++++l+GnndlL+lt+P++i aihrayfeaGaDi+
lcl|NCBI__GCF_000019845.1:WP_012384122.1 20 AERVLVLDGAMGTMIQQRKFTEADFRGErFKDWPSDLRGNNDLLTLTQPDAIVAIHRAYFEAGADII 86
589**************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
tntFnst i++adY++e++++eln+++a+lar++ade + + ++RfvaG+lGPtn++a++spdv+
lcl|NCBI__GCF_000019845.1:WP_012384122.1 87 GTNTFNSTRISQADYGMEELVAELNRESARLARQAADEAEAKDGRRRFVAGALGPTNRTASISPDVN 153
****************************************999999********************* PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p+fr vt+d+l++aY e++ +l++GG+D+l++et+fDtlnakaal a+ +v+e+ +++lP++isg+
lcl|NCBI__GCF_000019845.1:WP_012384122.1 154 NPGFRAVTFDDLRAAYAEAASALIEGGADILIVETIFDTLNAKAALAAIDDVYESLNVRLPVMISGT 220
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d sGrtLsGqt af sl+h + +++GLnCalGa e+r ++ els+ a++l+ ++PnaGLPn++
lcl|NCBI__GCF_000019845.1:WP_012384122.1 221 ITDLSGRTLSGQTPTAFWYSLRHVKPITIGLNCALGAREMRAHIAELSRVADTLICAYPNAGLPNEF 287
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g Yd+ pe +a+ + efae+gl+nivGGCCGttP+hi+aia+ v++i+prk +++e+ ++lsgle++
lcl|NCBI__GCF_000019845.1:WP_012384122.1 288 GLYDESPEYMASLVGEFAEAGLVNIVGGCCGTTPAHIHAIAKRVAGIAPRKIPAIEPLLRLSGLEPF 354
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
+++++ fvn+GeRtnv+Gs+kfrklik++++++al++a++qv +Gaq++D+n+De+llD+ea m+
lcl|NCBI__GCF_000019845.1:WP_012384122.1 355 TLTKDIRFVNVGERTNVTGSAKFRKLIKEGQFSAALDVARDQVVMGAQVIDVNMDEGLLDSEAVMRD 421
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+a+epdia+vP+m+Dss+f v+eaGLk+iqGk+ivnsislk+Gee+F++ ak +++yGaavvv
lcl|NCBI__GCF_000019845.1:WP_012384122.1 422 FLNLVAAEPDIARVPVMIDSSKFVVIEAGLKCIQGKGIVNSISLKEGEENFIQAAKAVHRYGAAVVV 488
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t+++k+ei++Ray++l++++gfppediifDpni+++atGieeh++y++dfiea+rei
lcl|NCBI__GCF_000019845.1:WP_012384122.1 489 MAFDEQGQADTRARKVEICSRAYDILVNRCGFPPEDIIFDPNIFAVATGIEEHNNYGVDFIEATREI 555
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
++++P ++isgGvsn+sFs+rgn++vR+a+hsvFLy+ai aG+Dmgivnag+l vy+++d+elre++
lcl|NCBI__GCF_000019845.1:WP_012384122.1 556 RQKFPLVHISGGVSNLSFSFRGNEPVRQAMHSVFLYHAIAAGMDMGIVNAGQLSVYEELDPELREAC 622
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l+rr+eate+Ll lae+ykg+ ++ k+++ +wr+ pve+RLe+alv+G++e+i++d+eear
lcl|NCBI__GCF_000019845.1:WP_012384122.1 623 EDVVLNRRPEATERLLALAENYKGQGTE--KQEKSLAWREEPVEKRLEHALVNGITEFIDQDVEEAR 687
***************************9..888999******************************* PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.....ks 732
+++l++iegpL++Gm+vvGdLFGsGkmfLPqvvksarvmk+avayL+P++e+ek+++ +s
lcl|NCBI__GCF_000019845.1:WP_012384122.1 688 LASTRTLDVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMKAAVAYLMPFMEAEKAANggavrSS 754
**********************************************************999***9** PP
TIGR02082 733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799
+Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP++kile+a+ ++ D+iglsGLi++sld
lcl|NCBI__GCF_000019845.1:WP_012384122.1 755 AGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAKILETARAEQVDCIGLSGLITPSLD 821
******************************************************************* PP
TIGR02082 800 emvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkkae 865
em +va e+er+g+++Pll+GGa++s+ h+avki+++Y g++vyv+das+av v++llse+++ +
lcl|NCBI__GCF_000019845.1:WP_012384122.1 822 EMCFVAAELEREGFDVPLLIGGATTSRVHTAVKIHPNYTrGQTVYVTDASRAVGTVQSLLSETSRGA 888
**************************************548************************** PP
TIGR02082 866 elekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellk 931
++e i++ey+++ +++ + +++ l++++ar++ f +d+ ++++p p+f G +++ ++ + el++
lcl|NCBI__GCF_000019845.1:WP_012384122.1 889 YIETIRAEYQKVSDAHRRAEAEKQRLPLQRARQNAFRPDWA-AYQPPRPTFTGARIFGSYdVGELVP 954
*****************************************.************************* PP
TIGR02082 932 yiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgdd 998
yiDw+++F +Welrg+yp l+d+++g+ ar+lf+da+++l+++++e+ +++v+G++Pa+ v+dd
lcl|NCBI__GCF_000019845.1:WP_012384122.1 955 YIDWTPFFQTWELRGRYPALLDDPKQGASARQLFDDAQAMLKRIVEEHWFDPKAVIGFWPANAVDDD 1021
******************************************************************* PP
TIGR02082 999 ieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeela 1064
i++yt+e++ +++at+ + ++ql +q d+ +l+laDf+a+++sG++Dy+g ++vtag +e++a
lcl|NCBI__GCF_000019845.1:WP_012384122.1 1022 IKLYTGESR---SEELATFFTLRQQLSKQGDKpNLALADFVAPRDSGKADYIGGFVVTAGAREEKIA 1085
*****9999...78889999999******9999********************************** PP
TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
+++ + +ddy+si+vkaladr+aea+ae +hervR+e+w+ya +enl +e+ + e+YrGirpa+GYp
lcl|NCBI__GCF_000019845.1:WP_012384122.1 1086 ERFAKANDDYGSIMVKALADRIAEAFAERMHERVRREFWAYAPDENLTNEERISESYRGIRPAPGYP 1152
******************************************************************* PP
TIGR02082 1132 acPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
a+Pdh+ekatl++Lleaer i + ltes+a++P +svsgly+a+pea Yf v
lcl|NCBI__GCF_000019845.1:WP_012384122.1 1153 AQPDHSEKATLFRLLEAERrISVSLTESFAMWPGSSVSGLYIAQPEAYYFGV 1204
**************************************************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1246 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: 0.11u 0.05s 00:00:00.16 Elapsed: 00:00:00.14
# Mc/sec: 10.20
//
[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