Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate YP_002827542.1 NGR_c30540 B12-dependent methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>NCBI__GCF_000018545.1:YP_002827542.1
Length = 1256
Score = 1472 bits (3812), Expect = 0.0
Identities = 756/1220 (61%), Positives = 907/1220 (74%), Gaps = 11/1220 (0%)
Query: 14 ERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAAIHNAYFE 73
ERIL++DG MGT IQ E FRGERF C +GNNDLL L++P+ I IH Y
Sbjct: 29 ERILIMDGAMGTEIQQLGFVEDHFRGERFGGCACHQQGNNDLLTLTQPKAIEEIHYRYAL 88
Query: 74 AGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKPRYVAGVL 133
AGADI+ETNTF+ST IA ADY ME + ++N A+LAR A A + R+VAG L
Sbjct: 89 AGADILETNTFSSTRIAQADYGMEDMVYDLNRDGARLARRAAKRAEAEDGRR-RFVAGAL 147
Query: 134 GPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDTLNAKAAV 193
GPTNRTASISPDVN+P +R ++FD L AY E + L++GGAD+ILIET+FDTLNAKAA+
Sbjct: 148 GPTNRTASISPDVNNPGYRAVSFDDLRLAYAEQVRGLIDGGADIILIETIFDTLNAKAAI 207
Query: 194 FAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLNCALGPDE 253
FA + F + LP+M+SGTITD SGRTLSGQT AF+ S+RHA T GLNCALG D
Sbjct: 208 FATQEVFAEKKIHLPVMVSGTITDLSGRTLSGQTPTAFWYSVRHAAPFTIGLNCALGADA 267
Query: 254 LRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNIVGGCCGT 313
+R ++ ELS +A+ V A+PNAGLPN FG YD +TMA QI + + G +NIVGGCCG+
Sbjct: 268 MRAHIDELSTVADTLVCAYPNAGLPNEFGRYDESPETMAAQIEAFVRDGLVNIVGGCCGS 327
Query: 314 TPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVTGSAKFKR 373
TP HI A++ AV+ PR++PEI RLSGLEP + ++ FVNVGERTNVTGSAKF++
Sbjct: 328 TPAHIRAIAEAVQKYPPRQVPEIERRMRLSGLEPFTLTDEIPFVNVGERTNVTGSAKFRK 387
Query: 374 LIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDIARVPIMI 433
LI Y+ ALDVAR QV NGAQIIDINMDEG++D+ AMV FLNL+A EPDIA VP+MI
Sbjct: 388 LITTGDYAAALDVARDQVANGAQIIDINMDEGLIDSTRAMVEFLNLVASEPDIACVPVMI 447
Query: 434 DSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFDEQGQADT 493
DSSKW+VIE GLKC+QGK +VNSIS+KEG +AF+HHA+L+R YGAAVVVMAFDE+GQAD+
Sbjct: 448 DSSKWEVIEAGLKCVQGKALVNSISLKEGEEAFLHHARLVRAYGAAVVVMAFDEKGQADS 507
Query: 494 RARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGACEDIKREL 553
RARK+EICRRAY++LTEEVGFPPEDIIFDPNIFAVATGI+EHNNY DFI A +I L
Sbjct: 508 RARKVEICRRAYRLLTEEVGFPPEDIIFDPNIFAVATGIDEHNNYGVDFIEATHEIIATL 567
Query: 554 PHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYDDLPAELR 613
PH +SGGVSN+SFSFRGN+PVREA+HAVFLY+AI+ GMDMGIVNAGQLA+YD + ELR
Sbjct: 568 PHVHVSGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYDAIDPELR 627
Query: 614 DAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYSLVKGITE 673
+A EDV+LNRR D TERLLE+AE+YRG + + WR W V KRLE++LV GITE
Sbjct: 628 EACEDVVLNRRPDATERLLEIAERYRG-QGGAQGKEKDLAWRQWPVAKRLEHALVNGITE 686
Query: 674 FIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLE 733
FIE DTEEAR A RP+ VIEGPLM GMNVVGDLFG GKMFLPQVVKSARVMKQAVA L
Sbjct: 687 FIEADTEEARLAAERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAVLL 746
Query: 734 PFIEASKEQG------KTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAE 787
P++EA K + GK+++ATVKGDVHDIGKNIVGVVL CNNYEI+DLGVMVP+
Sbjct: 747 PYMEAEKLANGGEGTRASAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPSA 806
Query: 788 KILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKAHTAVKIE 847
KIL A++ D IGLSGLITPSLDEMV+VA E+ER+GF IPLLIGGATTS+ HTAVKI
Sbjct: 807 KILEVARQEKVDAIGLSGLITPSLDEMVHVASELEREGFDIPLLIGGATTSRVHTAVKIN 866
Query: 848 QNYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPRTPPVTL 906
Y G TVYV +ASR VGVV++LLS RD + R EY V H R + + L
Sbjct: 867 PRYGLGQTVYVTDASRAVGVVSSLLSPEARDGYKETVRAEYLKVADAHARNEAEKRRLPL 926
Query: 907 EAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMTWSLAGKYPRILE 965
AR N DW AY P LG + E+ + L YIDWTPFF TW L G YPRIL+
Sbjct: 927 SQARANASKLDWDAYRPKTPSFLGTRVFESWDLAELARYIDWTPFFQTWELKGVYPRILD 986
Query: 966 DEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINV 1025
DE G A++LF DA ML+K+ AEK P+ VVG +PA GDDI ++ DE R +
Sbjct: 987 DEHQGPAARQLFADAQAMLEKIIAEKWFAPKAVVGFWPAGSAGDDIRLFTDERRERELAT 1046
Query: 1026 SHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEAQHDDYN 1084
LRQQ ++ G N LADFVAP SG+ DY+G F VT G+EE A+A+ FE +DDY+
Sbjct: 1047 FFTLRQQLAKRDGRPNVALADFVAPVESGRRDYLGGFVVTAGIEEVAIAERFERANDDYS 1106
Query: 1085 KIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPGYPACPE 1144
I+VKALADR AEAFAE +HE VRK WGYAP+E+ + +ELI E Y GIRPAPGYPA P+
Sbjct: 1107 SILVKALADRFAEAFAERMHEYVRKELWGYAPDESFTPQELIAEPYTGIRPAPGYPAQPD 1166
Query: 1145 HTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRDQVEDYA 1204
HTEK T++ LL+ E G++LTE++AMWPG+SVSG Y HPD+ Y+ VA+I+RDQVEDYA
Sbjct: 1167 HTEKETLFRLLDAEAAIGVRLTENYAMWPGSSVSGLYVGHPDAYYFGVAKIERDQVEDYA 1226
Query: 1205 RRKGMSVTEVERWLAPNLGY 1224
RK M V EVERWL+P L Y
Sbjct: 1227 TRKRMGVREVERWLSPILNY 1246
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: 3767
Number of extensions: 157
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1227
Length of database: 1256
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1208
Effective search space: 1424232
Effective search space used: 1424232
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 YP_002827542.1 NGR_c30540 (B12-dependent 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.26822.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 1740.0 0.0 0 1739.8 0.0 1.0 1 lcl|NCBI__GCF_000018545.1:YP_002827542.1 NGR_c30540 B12-dependent methion
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827542.1 NGR_c30540 B12-dependent methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1739.8 0.0 0 0 2 1182 .] 28 1214 .. 27 1214 .. 0.99
Alignments for each domain:
== domain 1 score: 1739.8 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDiv 67
+ril++DGamGt++q+ e++Frge + +a++++GnndlL+lt+P +i++ih +y aGaDi+
lcl|NCBI__GCF_000018545.1:YP_002827542.1 28 AERILIMDGAMGTEIQQLGFVEDHFRGErFGGCACHQQGNNDLLTLTQPKAIEEIHYRYALAGADIL 94
589*************************9************************************** PP
TIGR02082 68 etntFnsteialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdve 134
etntF+st ia+adY++ed +y+ln+ +a+lar++a+ + + ++RfvaG+lGPtn++a++spdv+
lcl|NCBI__GCF_000018545.1:YP_002827542.1 95 ETNTFSSTRIAQADYGMEDMVYDLNRDGARLARRAAKRAEAEDGRRRFVAGALGPTNRTASISPDVN 161
****************************************9999*********************** PP
TIGR02082 135 rpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgv 201
+p++r v +d+l+ aY eqv+gl+dGG+D++Liet+fDtlnakaa+fa++evf+ek+++lP+++sg+
lcl|NCBI__GCF_000018545.1:YP_002827542.1 162 NPGYRAVSFDDLRLAYAEQVRGLIDGGADIILIETIFDTLNAKAAIFATQEVFAEKKIHLPVMVSGT 228
******************************************************************* PP
TIGR02082 202 ivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnal 268
i+d sGrtLsGqt af s++ha +++GLnCalGad +r ++ els a++lv ++PnaGLPn++
lcl|NCBI__GCF_000018545.1:YP_002827542.1 229 ITDLSGRTLSGQTPTAFWYSVRHAAPFTIGLNCALGADAMRAHIDELSTVADTLVCAYPNAGLPNEF 295
******************************************************************* PP
TIGR02082 269 geYdltpeelakalkefaeegllnivGGCCGttPehiraiaeavkdikprkrqeleeksvlsgleal 335
g Yd+ pe++a++++ f+++gl+nivGGCCG+tP+hiraiaeav++ pr+++e+e +++lsgle++
lcl|NCBI__GCF_000018545.1:YP_002827542.1 296 GRYDESPETMAAQIEAFVRDGLVNIVGGCCGSTPAHIRAIAEAVQKYPPRQVPEIERRMRLSGLEPF 362
******************************************************************* PP
TIGR02082 336 kiaqessfvniGeRtnvaGskkfrklikaedyeealkiakqqveeGaqilDinvDevllDgeadmkk 402
++++e fvn+GeRtnv+Gs+kfrkli+ +dy +al++a++qv +Gaqi+Din+De+l D++++m++
lcl|NCBI__GCF_000018545.1:YP_002827542.1 363 TLTDEIPFVNVGERTNVTGSAKFRKLITTGDYAAALDVARDQVANGAQIIDINMDEGLIDSTRAMVE 429
******************************************************************* PP
TIGR02082 403 llsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkdGeerFlekaklikeyGaavvv 469
+l+l+asepdia vP+m+Dss++ev+eaGLk++qGka+vnsislk+Gee+Fl++a+l++ yGaavvv
lcl|NCBI__GCF_000018545.1:YP_002827542.1 430 FLNLVASEPDIACVPVMIDSSKWEVIEAGLKCVQGKALVNSISLKEGEEAFLHHARLVRAYGAAVVV 496
******************************************************************* PP
TIGR02082 470 mafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehdryaidfieairei 536
mafDe+Gqa+ +++k+ei++Ray+llte+vgfppediifDpni+++atGi+eh++y++dfiea++ei
lcl|NCBI__GCF_000018545.1:YP_002827542.1 497 MAFDEKGQADSRARKVEICRRAYRLLTEEVGFPPEDIIFDPNIFAVATGIDEHNNYGVDFIEATHEI 563
******************************************************************* PP
TIGR02082 537 keelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevv 603
+lP++++sgGvsn+sFs+rgn++vRea+h+vFLy+ai+aG+Dmgivnag+lavyd id+elre++
lcl|NCBI__GCF_000018545.1:YP_002827542.1 564 IATLPHVHVSGGVSNLSFSFRGNEPVREAMHAVFLYHAIQAGMDMGIVNAGQLAVYDAIDPELREAC 630
******************************************************************* PP
TIGR02082 604 edlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear 670
ed++l+rr++ate+Lle+ae+y+g+ ++ k ++ +wr++pv +RLe+alv+G++e+ie+d+eear
lcl|NCBI__GCF_000018545.1:YP_002827542.1 631 EDVVLNRRPDATERLLEIAERYRGQGGAQGK-EKDLAWRQWPVAKRLEHALVNGITEFIEADTEEAR 696
****************************777.66778****************************** PP
TIGR02082 671 kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed......k 731
+++pl++iegpL++Gm+vvGdLFG+GkmfLPqvvksarvmk+ava+L Py+e+ek ++
lcl|NCBI__GCF_000018545.1:YP_002827542.1 697 LAAERPLHVIEGPLMAGMNVVGDLFGAGKMFLPQVVKSARVMKQAVAVLLPYMEAEKLANggegtrA 763
*********************************************************9999999999 PP
TIGR02082 732 skGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksl 798
s+Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP +kile+a+++k D iglsGLi++sl
lcl|NCBI__GCF_000018545.1:YP_002827542.1 764 SAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPSAKILEVARQEKVDAIGLSGLITPSL 830
9****************************************************************** PP
TIGR02082 799 demvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkka 864
demv+va e+er+g++iPll+GGa++s+ h+avki+++Y g++vyv+das+av vv++lls ++++
lcl|NCBI__GCF_000018545.1:YP_002827542.1 831 DEMVHVASELEREGFDIPLLIGGATTSRVHTAVKINPRYGlGQTVYVTDASRAVGVVSSLLSPEARD 897
***************************************658************************* PP
TIGR02082 865 eelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieell 930
+ e +++ey ++ + +++ +++ l++++ar + +ld+ ++++ +p flGt+v+e+ ++el
lcl|NCBI__GCF_000018545.1:YP_002827542.1 898 GYKETVRAEYLKVADAHARNEAEKRRLPLSQARANASKLDWD-AYRPKTPSFLGTRVFESWdLAELA 963
*****************************************9.************************ PP
TIGR02082 931 kyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgd 997
yiDw+++F +Wel+g yp+il+de +g ar+lf+da+++l+k++aek +++vvG++Pa s gd
lcl|NCBI__GCF_000018545.1:YP_002827542.1 964 RYIDWTPFFQTWELKGVYPRILDDEHQGPAARQLFADAQAMLEKIIAEKWFAPKAVVGFWPAGSAGD 1030
******************************************************************* PP
TIGR02082 998 dieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeel 1063
di ++tde + +++at+ + ++ql + +r +++laDf+a+ esG +Dylg ++vtag+++ ++
lcl|NCBI__GCF_000018545.1:YP_002827542.1 1031 DIRLFTDERR---ERELATFFTLRQQLAKRDGRpNVALADFVAPVESGRRDYLGGFVVTAGIEEVAI 1094
*******999...567777777788888888888********************************* PP
TIGR02082 1064 akkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldkedllkerYrGirpafGY 1130
a+++e +ddy+silvkaladr+aea+ae +he vRkelwgya +e+ ++l+ e Y Girpa+GY
lcl|NCBI__GCF_000018545.1:YP_002827542.1 1095 AERFERANDDYSSILVKALADRFAEAFAERMHEYVRKELWGYAPDESFTPQELIAEPYTGIRPAPGY 1161
******************************************************************* PP
TIGR02082 1131 pacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
pa+Pdhtek tl++Ll+ae iG++lte++a++P +svsgly+ hp+a Yf v
lcl|NCBI__GCF_000018545.1:YP_002827542.1 1162 PAQPDHTEKETLFRLLDAEAaIGVRLTENYAMWPGSSVSGLYVGHPDAYYFGV 1214
***************************************************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1256 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 0.04s 00:00:00.12 Elapsed: 00:00:00.12
# Mc/sec: 11.71
//
[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