Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_011814940.1 HHAL_RS10885 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000015585.1:WP_011814940.1
Length = 1228
Score = 1524 bits (3946), Expect = 0.0
Identities = 770/1235 (62%), Positives = 956/1235 (77%), Gaps = 16/1235 (1%)
Query: 1 MSSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSK 60
M+ + +Q+R QL +RIL+LD GMGT IQ Y L EADFRGERF+D P +LKGNNDLLVL++
Sbjct: 1 MTDRSQQIRDQLAQRILILDCGMGTEIQKYPLEEADFRGERFSDHPSELKGNNDLLVLTR 60
Query: 61 PEVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTA 120
P++I I +AG DI+ETNTFNS ++ ADY E L E+N AAKLARA DE
Sbjct: 61 PDIIRDITRQNLDAGVDIVETNTFNSQVLSQADYGTEHLVDELNIEAAKLARAVCDEVEQ 120
Query: 121 RTPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILI 180
T PR+VAG +GPT +TASISPDVN+P R+ITFD L AY + + L+EGGADLILI
Sbjct: 121 ETGI-PRFVAGTMGPTGKTASISPDVNNPGHRDITFDQLFEAYAQQARGLLEGGADLILI 179
Query: 181 ETVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEA 240
ETVFDTLNAKAA++A++ FE G LP+MISGTITDASGRTLSGQT AF+NS+RHA
Sbjct: 180 ETVFDTLNAKAAIYALEEVFEESGRRLPVMISGTITDASGRTLSGQTAAAFWNSVRHARP 239
Query: 241 LTFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQ 300
++ GLNCALG ++LR ++QELS+IA+ +++ HPNAGLPN FGEYD + MAK +R +A+
Sbjct: 240 ISIGLNCALGAEDLRPHLQELSKIADTHISTHPNAGLPNEFGEYDQSPEEMAKIVRTFAE 299
Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEI-PVACRLSGLEPLNIGEDSLFVNV 359
G +NI+GGCCGT+P HIAA+ V+ APR++P++ P RLSGLEP NIG+DSLFVN+
Sbjct: 300 EGLINIIGGCCGTSPAHIAAIREQVKDFAPRQVPDLAPDVTRLSGLEPCNIGKDSLFVNI 359
Query: 360 GERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNL 419
GER NVTGSA+F+RLIKE Y AL+VA++QVENGAQIIDINMDEGMLD++ AM+ FLNL
Sbjct: 360 GERANVTGSARFRRLIKEGDYETALEVAKEQVENGAQIIDINMDEGMLDSKDAMIDFLNL 419
Query: 420 IAGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAA 479
+ EPDI+RVPIMIDSSKWD+IE+GLK IQGKG+VNSIS+KEG +AF+ A+ L+RYGAA
Sbjct: 420 VGSEPDISRVPIMIDSSKWDIIEEGLKRIQGKGLVNSISLKEGEEAFLQQARKLKRYGAA 479
Query: 480 VVVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYA 539
VVM FDE+GQADT R++EI RAY L + GF P DI+FD NIFAVATGIEEHNNYA
Sbjct: 480 AVVMCFDEKGQADTYERRLEIAERAYNALVND-GFEPADIVFDLNIFAVATGIEEHNNYA 538
Query: 540 QDFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNA 599
DFI A +K LPHA +SGG+SN+SFSFRGN+PVREA+H+VFLY+AI+ G+DM IVNA
Sbjct: 539 VDFIEATRWVKENLPHAKVSGGLSNLSFSFRGNEPVREAMHSVFLYHAIKAGLDMAIVNA 598
Query: 600 GQLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRG----SKTDDTANAQQAEWR 655
GQ+ +YD++ ELR+ EDVILNR +D T+RLLELAE+Y+G K +D A WR
Sbjct: 599 GQIEVYDEIDKELRELCEDVILNRHEDATDRLLELAERYKGQGGKKKEEDLA------WR 652
Query: 656 SWEVNKRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFL 715
V KRLE++L+KGIT++I+ D EEARQ+ RPI+VIEGPLMDGMN VGDLFGEGKMFL
Sbjct: 653 EEPVEKRLEHALIKGITDYIDVDVEEARQKHDRPIQVIEGPLMDGMNTVGDLFGEGKMFL 712
Query: 716 PQVVKSARVMKQAVAYLEPFIEASKE-QGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNN 774
PQVVKSARVMKQAV++L P+IEA K + G+++IATVKGDVHDIGKNIV VVLQCNN
Sbjct: 713 PQVVKSARVMKQAVSHLLPYIEAEKSGDDEPAGRVLIATVKGDVHDIGKNIVAVVLQCNN 772
Query: 775 YEIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGG 834
+E+ D+GVMVP E IL+ AKEV AD+IGLSGLITPSLDEM+ VA+EMERQGFT PLLIGG
Sbjct: 773 FEVHDIGVMVPTETILQKAKEVKADIIGLSGLITPSLDEMIGVAQEMERQGFTCPLLIGG 832
Query: 835 ATTSKAHTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQH 894
ATTS+ HTAVKI NYS P++YV++ASR VGV + L+S+TQ + + EY+ VR QH
Sbjct: 833 ATTSRVHTAVKIAPNYSAPSIYVKDASRAVGVASKLVSETQAEPYKQELAAEYQQVREQH 892
Query: 895 GRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMT 953
++ +T VT E A+ N DW A+ P + GVQ + + +E L IDWTPFF
Sbjct: 893 EARQKKTKWVTFEQAKQNATPIDWSAHQPIQPQKPGVQVLDDYPLEDLVERIDWTPFFAA 952
Query: 954 WSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEI 1013
W + G+YP+IL+DE G EA++LF DA ML ++ EK L+ R V GLFPAN G+D E+
Sbjct: 953 WQMRGQYPKILDDEKQGEEARKLFDDAQAMLRRIIDEKWLSARAVFGLFPANSTGEDTEV 1012
Query: 1014 YRDETRTHVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDAL 1072
Y DE R+ V+ HLRQQTEK G + LADF+APK SG D++GAFAVT G+ D
Sbjct: 1013 YADEQRSEVLATLCHLRQQTEKGEGKPHQSLADFIAPKDSGVLDWMGAFAVTAGVGIDEH 1072
Query: 1073 ADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQG 1132
FE DDY+ IM+KALADRLAEAFAE LHE+VRK +WGYA +ENLSNE++I+E YQG
Sbjct: 1073 VRRFEEAGDDYSAIMLKALADRLAEAFAESLHEQVRKDHWGYAADENLSNEDMIKERYQG 1132
Query: 1133 IRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAV 1192
IRPAPGYPACP+HTEK +WE+L VE++ G+ LTES AM P A+VSGWYF+HP+++Y+ V
Sbjct: 1133 IRPAPGYPACPDHTEKDRLWEILNVEENIGLTLTESRAMVPTAAVSGWYFAHPEARYFGV 1192
Query: 1193 AQIQRDQVEDYARRKGMSVTEVERWLAPNLGYDAD 1227
+I +DQVEDYA+RKGMS E ERWL PNLGY+ +
Sbjct: 1193 GKIFQDQVEDYAKRKGMSRKEAERWLGPNLGYEPE 1227
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: 3666
Number of extensions: 142
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: 1228
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1181
Effective search space: 1393580
Effective search space used: 1393580
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_011814940.1 HHAL_RS10885 (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.12663.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 1774.5 0.0 0 1774.3 0.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011814940.1 HHAL_RS10885 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015585.1:WP_011814940.1 HHAL_RS10885 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1774.3 0.0 0 0 2 1182 .] 13 1192 .. 12 1192 .. 0.99
Alignments for each domain:
== domain 1 score: 1774.3 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+ril+lD +mGt++q++ L+eadFrge ++d+++elkGnndlL+lt+P++i++i r+ ++aG Div
lcl|NCBI__GCF_000015585.1:WP_011814940.1 13 AQRILILDCGMGTEIQKYPLEEADFRGErFSDHPSELKGNNDLLVLTRPDIIRDITRQNLDAGVDIV 79
79***************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etntFns +++adY++e+++ eln +aaklar+v+de+++++ +RfvaG++GPt k+a++spdv+
lcl|NCBI__GCF_000015585.1:WP_011814940.1 80 ETNTFNSQVLSQADYGTEHLVDELNIEAAKLARAVCDEVEQETGIPRFVAGTMGPTGKTASISPDVN 146
******************************************************************* PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p++r++t+d+l +aY +q++gll+GG+Dl+LietvfDtlnakaa++a+eevfee gr+lP++isg+
lcl|NCBI__GCF_000015585.1:WP_011814940.1 147 NPGHRDITFDQLFEAYAQQARGLLEGGADLILIETVFDTLNAKAAIYALEEVFEESGRRLPVMISGT 213
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d+sGrtLsGqt +af +s++ha +++GLnCalGa++lr++++els++a++ +s++PnaGLPn++
lcl|NCBI__GCF_000015585.1:WP_011814940.1 214 ITDASGRTLSGQTAAAFWNSVRHARPISIGLNCALGAEDLRPHLQELSKIADTHISTHPNAGLPNEF 280
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqe.leeksvlsglea 334
geYd+ pee+ak+++ faeegl+ni+GGCCGt P+hi+ai e vkd +pr++++ ++ ++lsgle+
lcl|NCBI__GCF_000015585.1:WP_011814940.1 281 GEYDQSPEEMAKIVRTFAEEGLINIIGGCCGTSPAHIAAIREQVKDFAPRQVPDlAPDVTRLSGLEP 347
*****************************************************94566789****** PP
TIGR02082 335 lkiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmk 401
+i+++s fvniGeR nv+Gs++fr+lik++dye al++ak+qve+Gaqi+Din+De++lD++ +m
lcl|NCBI__GCF_000015585.1:WP_011814940.1 348 CNIGKDSLFVNIGERANVTGSARFRRLIKEGDYETALEVAKEQVENGAQIIDINMDEGMLDSKDAMI 414
******************************************************************* PP
TIGR02082 402 kllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavv 468
+l+l+ sepdi++vP+m+Dss+++++e GLk+iqGk++vnsislk+Gee+Fl++a+++k+yGaa+v
lcl|NCBI__GCF_000015585.1:WP_011814940.1 415 DFLNLVGSEPDISRVPIMIDSSKWDIIEEGLKRIQGKGLVNSISLKEGEEAFLQQARKLKRYGAAAV 481
******************************************************************* PP
TIGR02082 469 vmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieaire 535
vm fDe+Gqa+t+++++eia+Ray++l++ gf+p di+fD ni+++atGieeh++ya+dfiea+r+
lcl|NCBI__GCF_000015585.1:WP_011814940.1 482 VMCFDEKGQADTYERRLEIAERAYNALVN-DGFEPADIVFDLNIFAVATGIEEHNNYAVDFIEATRW 547
****************************9.8************************************ PP
TIGR02082 536 ikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrev 602
+ke+lP+ak+sgG+sn+sFs+rgn++vRea+hsvFLy+aikaGlDm+ivnag+++vyd+idkelre+
lcl|NCBI__GCF_000015585.1:WP_011814940.1 548 VKENLPHAKVSGGLSNLSFSFRGNEPVREAMHSVFLYHAIKAGLDMAIVNAGQIEVYDEIDKELREL 614
******************************************************************* PP
TIGR02082 603 vedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleea 669
+ed+il+r+++at++Llelae+ykg+ k k+++ +wr+ pve+RLe+al+kG++++i+ d+eea
lcl|NCBI__GCF_000015585.1:WP_011814940.1 615 CEDVILNRHEDATDRLLELAERYKGQGGK--KKEEDLAWREEPVEKRLEHALIKGITDYIDVDVEEA 679
****************************9..7778899***************************** PP
TIGR02082 670 rkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGk 735
r+k +p+++iegpL+dGm++vGdLFG+GkmfLPqvvksarvmk+av++L Py+e+ek+ d + +G+
lcl|NCBI__GCF_000015585.1:WP_011814940.1 680 RQKHDRPIQVIEGPLMDGMNTVGDLFGEGKMFLPQVVKSARVMKQAVSHLLPYIEAEKSGDdEPAGR 746
**********************************************************9653889** PP
TIGR02082 736 ivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemv 802
+++atvkGDvhDiGkniv vvL+cn++ev d+Gv+vP+e+il++ak+ kaD+iglsGLi++sldem+
lcl|NCBI__GCF_000015585.1:WP_011814940.1 747 VLIATVKGDVHDIGKNIVAVVLQCNNFEVHDIGVMVPTETILQKAKEVKADIIGLSGLITPSLDEMI 813
******************************************************************* PP
TIGR02082 803 evaeemerrgvkiPlllGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelek 869
va+emer+g++ Pll+GGa++s+ h+avkia++Y+++ +yvkdas+av v++kl+se++ +++ ++
lcl|NCBI__GCF_000015585.1:WP_011814940.1 814 GVAQEMERQGFTCPLLIGGATTSRVHTAVKIAPNYSAPSIYVKDASRAVGVASKLVSETQAEPYKQE 880
******************************************************************* PP
TIGR02082 870 ikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDw 935
+ +ey+++re+++ +++k++ ++ ++a+++ +d+s + ++ +p++ G++vl+++ +e+l++ iDw
lcl|NCBI__GCF_000015585.1:WP_011814940.1 881 LAAEYQQVREQHEARQKKTKWVTFEQAKQNATPIDWS-AHQPIQPQKPGVQVLDDYpLEDLVERIDW 946
*************************************.99*************************** PP
TIGR02082 936 kalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiy 1002
+++F +W++rg+ypkil+de++g+earklf+da+++l +++ ek l ar+v+GlfPa+s+g+d e+y
lcl|NCBI__GCF_000015585.1:WP_011814940.1 947 TPFFAAWQMRGQYPKILDDEKQGEEARKLFDDAQAMLRRIIDEKWLSARAVFGLFPANSTGEDTEVY 1013
******************************************************************* PP
TIGR02082 1003 tdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkle 1068
+de++ +++at+ + ++q+++ +++ +++laDfia+k+sG D++ga++vtag+g++e +++e
lcl|NCBI__GCF_000015585.1:WP_011814940.1 1014 ADEQR---SEVLATLCHLRQQTEKGEGKpHQSLADFIAPKDSGVLDWMGAFAVTAGVGIDEHVRRFE 1077
*9988...8999999999999999999999************************************* PP
TIGR02082 1069 akeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPd 1135
+ ddy++i++kaladrlaea+ae lhe+vRk++wgya++enl++ed++kerY+Girpa+GYpacPd
lcl|NCBI__GCF_000015585.1:WP_011814940.1 1078 EAGDDYSAIMLKALADRLAEAFAESLHEQVRKDHWGYAADENLSNEDMIKERYQGIRPAPGYPACPD 1144
******************************************************************* PP
TIGR02082 1136 htekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
htek +l+e+l++e+ iGl+ltes a+ P+a+vsg+yfahpea+Yf v
lcl|NCBI__GCF_000015585.1:WP_011814940.1 1145 HTEKDRLWEILNVEEnIGLTLTESRAMVPTAAVSGWYFAHPEARYFGV 1192
*************999******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1228 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: 13.53
//
[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