Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate SMc03112 SMc03112 B12-dependent methionine synthase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__Smeli:SMc03112
Length = 1257
Score = 1479 bits (3829), Expect = 0.0
Identities = 757/1232 (61%), Positives = 912/1232 (74%), Gaps = 11/1232 (0%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
S QL ERIL++DG MGT IQ E FRGERF C +GNNDLL L++P
Sbjct: 18 SEVFRQLAQAAAERILIMDGAMGTEIQQLGFVEDHFRGERFGGCACHQQGNNDLLTLTQP 77
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+ I IH Y AGADI+ETNTF+ST IA ADY ME + ++N A+LAR A A
Sbjct: 78 KAIEDIHYHYAIAGADILETNTFSSTRIAQADYGMEDMVYDLNRDGARLARRAAKRAEAE 137
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
+ R+VAG LGPTNRTASISPDVN+P +R ++FD L AY E + L++GGAD+ILIE
Sbjct: 138 DGRR-RFVAGALGPTNRTASISPDVNNPGYRAVSFDDLRLAYAEQVRGLIDGGADIILIE 196
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FA + F GV LP+MISGTITD SGRTLSGQT AF+ S+RHA+
Sbjct: 197 TIFDTLNAKAAIFATQEVFAEKGVRLPVMISGTITDLSGRTLSGQTPTAFWYSVRHADPF 256
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
T GLNCALG + +R ++ ELS +A+ V A+PNAGLPN FG YD + MA Q+ +A+
Sbjct: 257 TIGLNCALGANAMRAHIDELSAVADTLVCAYPNAGLPNEFGRYDESPEQMAAQVEGFARD 316
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
G +NIVGGCCG+TP HI A++ AV PR++PEI RLSGLEP + ++ FVNVGE
Sbjct: 317 GLVNIVGGCCGSTPAHIRAIAEAVAKYPPRRVPEIDRRMRLSGLEPFTLTDEIPFVNVGE 376
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTNVTGSAKF++LI Y+ ALDVAR QV NGAQIID+NMDEG++D++ MV FLNL+A
Sbjct: 377 RTNVTGSAKFRKLITAGDYAAALDVARDQVANGAQIIDVNMDEGLIDSKQVMVEFLNLVA 436
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
EPDIARVP+MIDSSKW+VIE GLKC+QGK +VNSIS+KEG AF+HHA+L+R YGAAVV
Sbjct: 437 SEPDIARVPVMIDSSKWEVIEAGLKCVQGKALVNSISLKEGEAAFLHHARLVRAYGAAVV 496
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDE+GQADT+ RK+EICRRAY++LTEEVGFPPEDIIFDPNIFAVATGIEEHNNY D
Sbjct: 497 VMAFDEKGQADTKTRKVEICRRAYRLLTEEVGFPPEDIIFDPNIFAVATGIEEHNNYGVD 556
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI A +I LPH +SGGVSN+SFSFRGN+PVREA+HA+FLY+AI+ GMDMGIVNAGQ
Sbjct: 557 FIEATHEIIAALPHVHVSGGVSNLSFSFRGNEPVREAMHAIFLYHAIQAGMDMGIVNAGQ 616
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
LA+YD + ELR+ EDV+LNRR D TERLLE+AE+YRG K + WR W V K
Sbjct: 617 LAVYDAIDPELRETCEDVVLNRRADSTERLLEIAERYRG-KGGSQGKEKDLAWREWPVEK 675
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LV GITEFIE DTEEAR A RP+ VIEGPLM GMNVVGDLFG GKMFLPQVVKS
Sbjct: 676 RLEHALVNGITEFIEADTEEARLAAERPLHVIEGPLMAGMNVVGDLFGSGKMFLPQVVKS 735
Query: 722 ARVMKQAVAYLEPFIEASK------EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNY 775
ARVMKQAVA L P +E K E ++ GK+++ATVKGDVHDIGKNIVGVVL CNNY
Sbjct: 736 ARVMKQAVAVLLPHMEEEKRANGGGEARESAGKILMATVKGDVHDIGKNIVGVVLACNNY 795
Query: 776 EIVDLGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGA 835
EI+DLGVMVP+ KIL A+E D++GLSGLITPSLDEM +VA E+ER+GF +PLLIGGA
Sbjct: 796 EIIDLGVMVPSAKILEVAREQKVDIVGLSGLITPSLDEMAHVASELEREGFDVPLLIGGA 855
Query: 836 TTSKAHTAVKIEQNYS-GPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQH 894
TTS+ HTAVKI YS G TVYV +ASR VGVV++LLS RD + R EY V H
Sbjct: 856 TTSRVHTAVKINPRYSLGQTVYVTDASRAVGVVSSLLSPEVRDSYKKTVRAEYLKVADAH 915
Query: 895 GRKKPRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVEA-SIETLRNYIDWTPFFMT 953
R + + L AR N F DW A+ P V LG + E + L YIDWTPFF T
Sbjct: 916 ARNEAEKRRLPLSQARANAFRIDWDAHQPKVPSFLGTRVFEGWDLAELARYIDWTPFFQT 975
Query: 954 WSLAGKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEI 1013
W L G +P+IL+DE G A++LF+DA M++K+ AE P+ V+G +PA +GDD+ +
Sbjct: 976 WELKGVFPKILDDERQGAAARQLFEDAQAMVEKIVAEAWFAPKAVIGFWPAASMGDDVRL 1035
Query: 1014 YRDETRTHVINVSHHLRQQ-TEKTGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDAL 1072
+ DE R + LRQQ ++ G N LADFVAP SGK DY+G F VT G+EE A+
Sbjct: 1036 FADEVREAELATFFTLRQQMVKRDGRPNVALADFVAPAASGKRDYVGGFVVTAGIEEVAI 1095
Query: 1073 ADAFEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQG 1132
A+ FE +DDY+ IMVKALADR AEAFAE +HE VRK WGYAP+E + +ELI E Y G
Sbjct: 1096 AERFERANDDYSSIMVKALADRFAEAFAERMHEYVRKELWGYAPDEAFTPQELIAEPYAG 1155
Query: 1133 IRPAPGYPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAV 1192
IRPAPGYPA P+HTEK T++ LL+ E G++LTES+AMWPG+SVSG Y HPDS Y+ V
Sbjct: 1156 IRPAPGYPAQPDHTEKETLFRLLDAEAAIGVRLTESYAMWPGSSVSGLYVGHPDSYYFGV 1215
Query: 1193 AQIQRDQVEDYARRKGMSVTEVERWLAPNLGY 1224
A+I+RDQVEDYA RK MSV EVERWL+P L Y
Sbjct: 1216 AKIERDQVEDYADRKRMSVREVERWLSPILNY 1247
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: 3774
Number of extensions: 164
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: 1257
Length adjustment: 48
Effective length of query: 1179
Effective length of database: 1209
Effective search space: 1425411
Effective search space used: 1425411
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 SMc03112 SMc03112 (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.4684.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 1741.4 0.0 0 1741.2 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc03112 SMc03112 B12-dependent methionin
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03112 SMc03112 B12-dependent methionine synthase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1741.2 0.0 0 0 2 1182 .] 29 1215 .. 28 1215 .. 0.99
Alignments for each domain:
== domain 1 score: 1741.2 bits; conditional E-value: 0
TIGR02082 2 nkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFn 73
+ril++DGamGt++q+ e++Frge + +a++++GnndlL+lt+P +i++ih +y aGaDi+etntF+
lcl|FitnessBrowser__Smeli:SMc03112 29 AERILIMDGAMGTEIQQLGFVEDHFRGErFGGCACHQQGNNDLLTLTQPKAIEDIHYHYAIAGADILETNTFS 101
589*************************9******************************************** PP
TIGR02082 74 steialadYdledkayelnkkaaklarevadeftltpekkRfvaGslGPtnklatlspdverpefrnvtydel 146
st ia+adY++ed +y+ln+ +a+lar++a+ + + ++RfvaG+lGPtn++a++spdv++p++r v +d+l
lcl|FitnessBrowser__Smeli:SMc03112 102 STRIAQADYGMEDMVYDLNRDGARLARRAAKRAEAEDGRRRFVAGALGPTNRTASISPDVNNPGYRAVSFDDL 174
**********************************9999*********************************** PP
TIGR02082 147 vdaYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtleafl 219
+ aY eqv+gl+dGG+D++Liet+fDtlnakaa+fa++evf+ekg++lP++isg+i+d sGrtLsGqt af
lcl|FitnessBrowser__Smeli:SMc03112 175 RLAYAEQVRGLIDGGADIILIETIFDTLNAKAAIFATQEVFAEKGVRLPVMISGTITDLSGRTLSGQTPTAFW 247
************************************************************************* PP
TIGR02082 220 aslehaeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeeglln 292
s++ha+ +++GLnCalGa+ +r ++ els+ a++lv ++PnaGLPn++g Yd+ pe++a++++ fa++gl+n
lcl|FitnessBrowser__Smeli:SMc03112 248 YSVRHADPFTIGLNCALGANAMRAHIDELSAVADTLVCAYPNAGLPNEFGRYDESPEQMAAQVEGFARDGLVN 320
************************************************************************* PP
TIGR02082 293 ivGGCCGttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikae 365
ivGGCCG+tP+hiraiaeav++ pr+++e++ +++lsgle++++++e fvn+GeRtnv+Gs+kfrkli+a+
lcl|FitnessBrowser__Smeli:SMc03112 321 IVGGCCGSTPAHIRAIAEAVAKYPPRRVPEIDRRMRLSGLEPFTLTDEIPFVNVGERTNVTGSAKFRKLITAG 393
************************************************************************* PP
TIGR02082 366 dyeealkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGk 438
dy +al++a++qv +Gaqi+D+n+De+l D+++ m+++l+l+asepdia+vP+m+Dss++ev+eaGLk++qGk
lcl|FitnessBrowser__Smeli:SMc03112 394 DYAAALDVARDQVANGAQIIDVNMDEGLIDSKQVMVEFLNLVASEPDIARVPVMIDSSKWEVIEAGLKCVQGK 466
************************************************************************* PP
TIGR02082 439 aivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpn 511
a+vnsislk+Ge++Fl++a+l++ yGaavvvmafDe+Gqa+t+ +k+ei++Ray+llte+vgfppediifDpn
lcl|FitnessBrowser__Smeli:SMc03112 467 ALVNSISLKEGEAAFLHHARLVRAYGAAVVVMAFDEKGQADTKTRKVEICRRAYRLLTEEVGFPPEDIIFDPN 539
************************************************************************* PP
TIGR02082 512 iltiatGieehdryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgiv 584
i+++atGieeh++y++dfiea++ei lP++++sgGvsn+sFs+rgn++vRea+h++FLy+ai+aG+Dmgiv
lcl|FitnessBrowser__Smeli:SMc03112 540 IFAVATGIEEHNNYGVDFIEATHEIIAALPHVHVSGGVSNLSFSFRGNEPVREAMHAIFLYHAIQAGMDMGIV 612
************************************************************************* PP
TIGR02082 585 nagklavyddidkelrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkG 657
nag+lavyd id+elre++ed++l+rr ++te+Lle+ae+y+g+ ++ k ++ +wr++pve+RLe+alv+G
lcl|FitnessBrowser__Smeli:SMc03112 613 NAGQLAVYDAIDPELRETCEDVVLNRRADSTERLLEIAERYRGKGGSQGK-EKDLAWREWPVEKRLEHALVNG 684
**********************************************9777.66778***************** PP
TIGR02082 658 eregieedleearkklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed 730
++e+ie+d+eear +++pl++iegpL++Gm+vvGdLFGsGkmfLPqvvksarvmk+ava+L P++e+ek ++
lcl|FitnessBrowser__Smeli:SMc03112 685 ITEFIEADTEEARLAAERPLHVIEGPLMAGMNVVGDLFGSGKMFLPQVVKSARVMKQAVAVLLPHMEEEKRAN 757
**********************************************************************999 PP
TIGR02082 731 ......kskGkivlatvkGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivks 797
+s+Gki++atvkGDvhDiGkniv+vvL+cn+ye++dlGv+vP +kile+a+++k D++glsGLi++s
lcl|FitnessBrowser__Smeli:SMc03112 758 gggearESAGKILMATVKGDVHDIGKNIVGVVLACNNYEIIDLGVMVPSAKILEVAREQKVDIVGLSGLITPS 830
9999999****************************************************************** PP
TIGR02082 798 ldemvevaeemerrgvkiPlllGGaalskahvavkiaekYk.gevvyvkdaseavkvvdkllsekkkaeelek 869
ldem++va e+er+g+++Pll+GGa++s+ h+avki+++Y+ g++vyv+das+av vv++lls + ++++ +
lcl|FitnessBrowser__Smeli:SMc03112 831 LDEMAHVASELEREGFDVPLLIGGATTSRVHTAVKINPRYSlGQTVYVTDASRAVGVVSSLLSPEVRDSYKKT 903
****************************************978****************************** PP
TIGR02082 870 ikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvq 941
+++ey ++ + +++ +++ l++++ar + f +d+ + ++ +p flGt+v+e ++el yiDw+++F +
lcl|FitnessBrowser__Smeli:SMc03112 904 VRAEYLKVADAHARNEAEKRRLPLSQARANAFRIDWD-AHQPKVPSFLGTRVFEGWdLAELARYIDWTPFFQT 975
************************************9.99********************************* PP
TIGR02082 942 WelrgkypkilkdeleglearklfkdakelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpi 1014
Wel+g +pkil+de +g+ ar+lf+da+++++k++ae +++v+G++Pa s+gdd+ +++de + ++
lcl|FitnessBrowser__Smeli:SMc03112 976 WELKGVFPKILDDERQGAAARQLFEDAQAMVEKIVAEAWFAPKAVIGFWPAASMGDDVRLFADEVR---EAEL 1045
****************************************************************99...4455 PP
TIGR02082 1015 atvrekleqlrqqsdr.ylclaDfiaskesGikDylgallvtaglgaeelakkleakeddydsilvkaladrl 1086
at+ + ++q+ + +r +++laDf+a+ +sG++Dy+g ++vtag+++ ++a+++e +ddy+si+vkaladr+
lcl|FitnessBrowser__Smeli:SMc03112 1046 ATFFTLRQQMVKRDGRpNVALADFVAPAASGKRDYVGGFVVTAGIEEVAIAERFERANDDYSSIMVKALADRF 1118
66666666666666666******************************************************** PP
TIGR02082 1087 aealaellhervRkelwgyaeeenldkedllkerYrGirpafGYpacPdhtekatlleLleaer.iGlkltes 1158
aea+ae +he vRkelwgya +e+ ++l+ e Y Girpa+GYpa+Pdhtek tl++Ll+ae iG++ltes
lcl|FitnessBrowser__Smeli:SMc03112 1119 AEAFAERMHEYVRKELWGYAPDEAFTPQELIAEPYAGIRPAPGYPAQPDHTEKETLFRLLDAEAaIGVRLTES 1191
************************************************************************* PP
TIGR02082 1159 lalaPeasvsglyfahpeakYfav 1182
+a++P +svsgly+ hp++ Yf v
lcl|FitnessBrowser__Smeli:SMc03112 1192 YAMWPGSSVSGLYVGHPDSYYFGV 1215
**********************76 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1257 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: 0.13u 0.04s 00:00:00.17 Elapsed: 00:00:00.16
# Mc/sec: 9.22
//
[ok]
This GapMind analysis is from Apr 09 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