Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate WP_012334098.1 M446_RS20885 methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000019365.1:WP_012334098.1
Length = 1247
Score = 1478 bits (3827), Expect = 0.0
Identities = 758/1230 (61%), Positives = 922/1230 (74%), Gaps = 19/1230 (1%)
Query: 8 LRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAI 67
LR + ERILVLDG MGTMIQ +L EADFRG+RF D D +GNNDLL+L++PE I I
Sbjct: 16 LRKRAAERILVLDGAMGTMIQRLKLGEADFRGKRFLDHAHDQRGNNDLLILTQPEAIRQI 75
Query: 68 HNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPR 127
H YF AGAD++ETNTF+ T IA ADY ME++ E+N A+LAR A E R + R
Sbjct: 76 HLDYFLAGADVVETNTFSGTAIAQADYGMEAIVRELNREGARLAREAAVE-AERRDGRRR 134
Query: 128 YVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTL 187
+VAG +GPTNRT SISPDVN+P +R++TFD + AY E + L+EGG+DL+LIET+FDTL
Sbjct: 135 FVAGAIGPTNRTLSISPDVNNPGYRSVTFDQVRDAYAEQVRGLIEGGSDLVLIETIFDTL 194
Query: 188 NAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNC 247
NAKAA+ A F +GV LPIMISGTITD SGRTLSGQT AF++SLRHAE LTFGLNC
Sbjct: 195 NAKAAIAATWQVFGEMGVRLPIMISGTITDLSGRTLSGQTPSAFWHSLRHAEPLTFGLNC 254
Query: 248 ALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIV 307
ALG E+R ++ ELSR+ + V A+PNAGLPN FG YD + M + E+A +G +N+V
Sbjct: 255 ALGAREMRAHISELSRVCDTLVCAYPNAGLPNEFGLYDESPEAMGALVGEFAGSGLVNMV 314
Query: 308 GGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTG 367
GGCCGTTP HI A++ AV G APR++PE+P RLSGLEP + ++ FVNVGERTNVTG
Sbjct: 315 GGCCGTTPDHIRAIAEAVAGKAPRRVPEVPRLMRLSGLEPFTLTKEIPFVNVGERTNVTG 374
Query: 368 SAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIA 427
SAKF++L+ Y+ ALDVAR QV GAQ+ID+NMDEG+LD+ AAMV FLNL+A EPDIA
Sbjct: 375 SAKFRKLVTSGDYAAALDVARDQVAAGAQVIDVNMDEGLLDSRAAMVEFLNLVAAEPDIA 434
Query: 428 RVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDE 487
RVP+M+DSSK++VIE GLKCIQGK IVNSIS+KEG + F+ A++ R YGAAVVVMAFDE
Sbjct: 435 RVPVMVDSSKFEVIEAGLKCIQGKPIVNSISLKEGKEKFLTEARICRAYGAAVVVMAFDE 494
Query: 488 QGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACE 547
QGQADT RK+ IC RAY+ILTEEVGFPPEDIIFDPNIFAVATGIEEH+ Y FI A
Sbjct: 495 QGQADTLERKVAICTRAYRILTEEVGFPPEDIIFDPNIFAVATGIEEHDGYGVAFIEAAR 554
Query: 548 DIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDD 607
I+ LPHA ISGGVSN+SF+FRGN+PVREA+HAVFLY+AIR GMDMGIVNAGQLA+YD+
Sbjct: 555 QIRETLPHAHISGGVSNLSFAFRGNEPVREAMHAVFLYHAIRAGMDMGIVNAGQLAVYDE 614
Query: 608 LPAELRDAVEDVILNRRDDGTERLLELAEKYRGS----KTDDTANAQQAEWRSWEVNKRL 663
L ELRD EDV+LNRR D TERLLE A K++G +T D A WR V KRL
Sbjct: 615 LDPELRDLCEDVVLNRRPDATERLLEQAAKFKGGGAQLRTADLA------WREAPVEKRL 668
Query: 664 EYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSAR 723
E++LV GITE+IE DTEEAR+ ATRP++VIEGPLM GMNVVGDLFG GKMFLPQVVKSAR
Sbjct: 669 EHALVNGITEYIEADTEEARRTATRPLDVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSAR 728
Query: 724 VMKQAVAYLEPFIEASKEQG-----KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIV 778
VMKQAVAYL PF+E K + GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+
Sbjct: 729 VMKQAVAYLMPFMEEEKRANGGTGRQAAGKVLMATVKGDVHDIGKNIVGVVLACNNYEII 788
Query: 779 DLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTS 838
DLGVMVPA KIL TA++ D++GLSGLITPSLDEMV+VA EMER+GF +PLLIGGATTS
Sbjct: 789 DLGVMVPAAKILDTARKEKVDIVGLSGLITPSLDEMVHVASEMEREGFEVPLLIGGATTS 848
Query: 839 KAHTAVKIEQNYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRK 897
+ HTAVKI Y+ G VYV +ASR VGVV++LLS + + R EY+ V H R
Sbjct: 849 RVHTAVKIHPAYAKGQAVYVTDASRAVGVVSSLLSPETKAATIEGVRAEYKRVAEAHARS 908
Query: 898 KPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSL 956
+ + L AR N F ++ Y P G + + + L YIDWTPF T+
Sbjct: 909 EADKQRLPLAKARANPFRAEFSTYRPAKPSFTGTRVFRSYDVAELVPYIDWTPFLQTYEF 968
Query: 957 AGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRD 1016
G++P +L+D V G A+ LF DA ML ++ E+ NP+ V+G +PAN VGDDI ++
Sbjct: 969 KGRFPALLDDPVQGPAARALFDDAQAMLARIVEERWFNPKAVIGFWPANAVGDDIRLFTG 1028
Query: 1017 ETRTHVINVSHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADA 1075
E+RT + H LRQQ +++ G N CL+DFVAP SG DY+G F VT GLEE +A+
Sbjct: 1029 ESRTDRLATFHGLRQQLSKRDGRPNTCLSDFVAPLDSGVPDYVGGFVVTAGLEEVRIAER 1088
Query: 1076 FEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRP 1135
FE Q+DDY I+VKALADR+AEAFAE +HERVRK +WGYA +E + +L+ E YQGIRP
Sbjct: 1089 FERQNDDYRSILVKALADRIAEAFAERMHERVRKEFWGYAADETFAPADLVLEEYQGIRP 1148
Query: 1136 APGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQI 1195
APGYPA P+HTEKAT+++LL+ E G+KLTES+AMWPG+SVSG Y +HP + Y+ VA++
Sbjct: 1149 APGYPAQPDHTEKATLFDLLQAEPRIGVKLTESYAMWPGSSVSGLYLAHPGAHYFGVAKV 1208
Query: 1196 QRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
+RDQVEDYA RKGM V EVERWL P L YD
Sbjct: 1209 ERDQVEDYAARKGMDVAEVERWLGPILNYD 1238
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: 3692
Number of extensions: 152
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: 1247
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1199
Effective search space: 1413621
Effective search space used: 1413621
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_012334098.1 M446_RS20885 (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.30861.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 1728.0 0.0 0 1727.8 0.0 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012334098.1 M446_RS20885 methionine synthase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019365.1:WP_012334098.1 M446_RS20885 methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1727.8 0.0 0 0 2 1182 .] 21 1205 .. 20 1205 .. 0.99
Alignments for each domain:
== domain 1 score: 1727.8 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+rilvlDGamGt++q+ +L eadFrg+ + d+a +++GnndlL lt+Pe+i++ih +yf aGaD+v
lcl|NCBI__GCF_000019365.1:WP_012334098.1 21 AERILVLDGAMGTMIQRLKLGEADFRGKrFLDHAHDQRGNNDLLILTQPEAIRQIHLDYFLAGADVV 87
589**************************************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etntF++t ia+adY++e+ ++eln+++a+lare+a e ++ ++RfvaG++GPtn++ ++spdv+
lcl|NCBI__GCF_000019365.1:WP_012334098.1 88 ETNTFSGTAIAQADYGMEAIVRELNREGARLAREAAVEAERRDGRRRFVAGAIGPTNRTLSISPDVN 154
****************************************99999********************** PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p++r vt+d+++daY eqv+gl++GG Dl+Liet+fDtlnakaa+ a+ +vf e g++lPi+isg+
lcl|NCBI__GCF_000019365.1:WP_012334098.1 155 NPGYRSVTFDQVRDAYAEQVRGLIEGGSDLVLIETIFDTLNAKAAIAATWQVFGEMGVRLPIMISGT 221
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d sGrtLsGqt af +sl+hae l++GLnCalGa e+r ++ els+ ++lv ++PnaGLPn++
lcl|NCBI__GCF_000019365.1:WP_012334098.1 222 ITDLSGRTLSGQTPSAFWHSLRHAEPLTFGLNCALGAREMRAHISELSRVCDTLVCAYPNAGLPNEF 288
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g Yd+ pe + + + efa gl+n+vGGCCGttP+hiraiaeav++ +pr+++e++ ++lsgle++
lcl|NCBI__GCF_000019365.1:WP_012334098.1 289 GLYDESPEAMGALVGEFAGSGLVNMVGGCCGTTPDHIRAIAEAVAGKAPRRVPEVPRLMRLSGLEPF 355
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
++++e fvn+GeRtnv+Gs+kfrkl++ +dy +al++a++qv Gaq++D+n+De+llD++a+m++
lcl|NCBI__GCF_000019365.1:WP_012334098.1 356 TLTKEIPFVNVGERTNVTGSAKFRKLVTSGDYAAALDVARDQVAAGAQVIDVNMDEGLLDSRAAMVE 422
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+a+epdia+vP+m+Dss+fev+eaGLk+iqGk ivnsislk+G+e+Fl +a++ + yGaavvv
lcl|NCBI__GCF_000019365.1:WP_012334098.1 423 FLNLVAAEPDIARVPVMVDSSKFEVIEAGLKCIQGKPIVNSISLKEGKEKFLTEARICRAYGAAVVV 489
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+t ++k+ i++Ray++lte+vgfppediifDpni+++atGieehd y+++fiea r+i
lcl|NCBI__GCF_000019365.1:WP_012334098.1 490 MAFDEQGQADTLERKVAICTRAYRILTEEVGFPPEDIIFDPNIFAVATGIEEHDGYGVAFIEAARQI 556
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
+e+lP+a+isgGvsn+sF++rgn++vRea+h+vFLy+ai+aG+Dmgivnag+lavyd++d+elr+++
lcl|NCBI__GCF_000019365.1:WP_012334098.1 557 RETLPHAHISGGVSNLSFAFRGNEPVREAMHAVFLYHAIRAGMDMGIVNAGQLAVYDELDPELRDLC 623
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l+rr++ate+Lle a ++kg ++ ++ +wr+ pve+RLe+alv+G++e+ie+d+eear
lcl|NCBI__GCF_000019365.1:WP_012334098.1 624 EDVVLNRRPDATERLLEQAAKFKGGGAQ--LRTADLAWREAPVEKRLEHALVNGITEYIEADTEEAR 688
*************************999..778999******************************* PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.....ks 732
+++++pl++iegpL++Gm+vvGdLFGsGkmfLPqvvksarvmk+avayL+P++e+ek ++ ++
lcl|NCBI__GCF_000019365.1:WP_012334098.1 689 RTATRPLDVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMKQAVAYLMPFMEEEKRANggtgrQA 755
*********************************************************999999999* PP
TIGR02082 733 kGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksld 799
+Gk+++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP++kil++a+k+k D++glsGLi++sld
lcl|NCBI__GCF_000019365.1:WP_012334098.1 756 AGKVLMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPAAKILDTARKEKVDIVGLSGLITPSLD 822
******************************************************************* PP
TIGR02082 800 emvevaeemerrgvkiPlllGGaalskahvavkiaekY.kgevvyvkdaseavkvvdkllsekkkae 865
emv+va emer+g+++Pll+GGa++s+ h+avki+++Y kg+ vyv+das+av vv++lls ++ka+
lcl|NCBI__GCF_000019365.1:WP_012334098.1 823 EMVHVASEMEREGFEVPLLIGGATTSRVHTAVKIHPAYaKGQAVYVTDASRAVGVVSSLLSPETKAA 889
**************************************679************************** PP
TIGR02082 866 elekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellk 931
+e +++ey+ + e + +++ ++ l++++ar + f + s +++++p f Gt+v++++ ++el++
lcl|NCBI__GCF_000019365.1:WP_012334098.1 890 TIEGVRAEYKRVAEAHARSEADKQRLPLAKARANPFRAEFS-TYRPAKPSFTGTRVFRSYdVAELVP 955
*****************************************.9************************ PP
TIGR02082 932 yiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgdd 998
yiDw+++ ++e++g++p l+d+++g ar lf+da+++l ++++e+ ++++v+G++Pa+ vgdd
lcl|NCBI__GCF_000019365.1:WP_012334098.1 956 YIDWTPFLQTYEFKGRFPALLDDPVQGPAARALFDDAQAMLARIVEERWFNPKAVIGFWPANAVGDD 1022
******************************************************************* PP
TIGR02082 999 ieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeela 1064
i ++t+e++ t+ +at++ ++ql + +r ++cl+Df+a+ +sG Dy+g ++vtagl++ +a
lcl|NCBI__GCF_000019365.1:WP_012334098.1 1023 IRLFTGESR---TDRLATFHGLRQQLSKRDGRpNTCLSDFVAPLDSGVPDYVGGFVVTAGLEEVRIA 1086
*****9998...999***********9999999********************************** PP
TIGR02082 1065 kkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGYp 1131
+++e ++ddy silvkaladr+aea+ae +hervRke+wgya++e + +dl+ e+Y+Girpa+GYp
lcl|NCBI__GCF_000019365.1:WP_012334098.1 1087 ERFERQNDDYRSILVKALADRIAEAFAERMHERVRKEFWGYAADETFAPADLVLEEYQGIRPAPGYP 1153
******************************************************************* PP
TIGR02082 1132 acPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
a+Pdhtekatl++Ll+ae iG+kltes+a++P +svsgly+ahp a+Yf v
lcl|NCBI__GCF_000019365.1:WP_012334098.1 1154 AQPDHTEKATLFDLLQAEPrIGVKLTESYAMWPGSSVSGLYLAHPGAHYFGV 1205
******************88******************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1247 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: 0.12u 0.04s 00:00:00.16 Elapsed: 00:00:00.16
# Mc/sec: 9.07
//
[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