Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate Dsui_0779 Dsui_0779 5-methyltetrahydrofolate--homocysteine methyltransferase
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__PS:Dsui_0779
Length = 1226
Score = 1505 bits (3897), Expect = 0.0
Identities = 767/1224 (62%), Positives = 934/1224 (76%), Gaps = 13/1224 (1%)
Query: 7 QLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKPEVIAA 66
+L A L +R+L+LDG MGTMIQ + L E D+RG RFAD DLKGNNDLL+L++PEVI
Sbjct: 8 ELSALLQQRLLILDGAMGTMIQRHGLTEKDYRGTRFADHAHDLKGNNDLLLLTRPEVIRG 67
Query: 67 IHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTARTPEKP 126
IH Y AGADI+ETNTFN+T ++ ADY++E++ E+N A A+LAR DE+TA+ P KP
Sbjct: 68 IHAEYLAAGADILETNTFNATKVSQADYKLEAIVYELNVAGARLAREVCDEFTAKNPAKP 127
Query: 127 RYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIETVFDT 186
R+VAGVLGPT+RTASISPDVNDP +RN+TFD LV Y E+ + L +GGAD++L+ETVFDT
Sbjct: 128 RFVAGVLGPTSRTASISPDVNDPGYRNVTFDELVENYLEAIRGLTDGGADILLVETVFDT 187
Query: 187 LNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEALTFGLN 246
LNAKAA+FA++T F+ +G P+MISGTITDASGRTLSGQT EAF+NSL H L+FGLN
Sbjct: 188 LNAKAALFAIETFFDKVGRRWPVMISGTITDASGRTLSGQTAEAFWNSLNHIRPLSFGLN 247
Query: 247 CALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQAGFLNI 306
CALG ELRQYV+ELSR+ +C+V+AHPNAGLPNAFG YD + +A++I +WA+ GF+NI
Sbjct: 248 CALGAKELRQYVEELSRVCDCFVSAHPNAGLPNAFGGYDETPEQLAEEIADWARHGFVNI 307
Query: 307 VGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGERTNVT 366
VGGCCGT+P HIAA+++ V G+APR +P I RLSGLEP N+G DSL+VNVGERTNVT
Sbjct: 308 VGGCCGTSPDHIAAIAKMVAGIAPRAIPAIEPQLRLSGLEPFNVGPDSLYVNVGERTNVT 367
Query: 367 GSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIAGEPDI 426
GS F R+I E +Y +AL VARQQVENGAQ+IDINMDE MLD+ AAM +FL LIA EPDI
Sbjct: 368 GSKAFARMILEGRYDDALAVARQQVENGAQVIDINMDEAMLDSVAAMEKFLKLIASEPDI 427
Query: 427 ARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVVVMAFD 486
+RVPIM+DSSKW+VIE GLKCIQGKGIVNSISMKEG F+ AKL RRYGAAV+VMAFD
Sbjct: 428 SRVPIMLDSSKWEVIETGLKCIQGKGIVNSISMKEGEAKFLEQAKLARRYGAAVIVMAFD 487
Query: 487 EQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQDFIGAC 546
E+GQADT ARK EIC+RAY +L +GFP +DIIFDPNIFA+ATGIEEH+NYA DFI A
Sbjct: 488 EKGQADTYARKTEICKRAYDLLV-GIGFPAQDIIFDPNIFAIATGIEEHDNYAVDFINAT 546
Query: 547 EDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQLAIYD 606
I+ LPHA ISGGVSNVSFSFRGNDPVREAIH VFLY+AI+ GM MGIVNAG L +YD
Sbjct: 547 RWIRENLPHAQISGGVSNVSFSFRGNDPVREAIHTVFLYHAIQAGMTMGIVNAGMLGVYD 606
Query: 607 DLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNKRLEYS 666
DL ELR VEDV+LNR E L+E A+ + K DT WR+ V KRLE++
Sbjct: 607 DLEPELRQKVEDVVLNRHPGAGEALVEFAQTVKEGKAKDT--GPDLTWRTLPVEKRLEHA 664
Query: 667 LVKGITEFIEQDTEEARQQATR----PIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKSA 722
LVKGITEF+ DTEE R P+ VIEGPLM+GMN VGDLFG GKMFLPQVVKSA
Sbjct: 665 LVKGITEFVVADTEEVRAALAAAGKPPLAVIEGPLMNGMNTVGDLFGAGKMFLPQVVKSA 724
Query: 723 RVMKQAVAYLEPFIEASKEQ--GKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
RVMKQAVA+L P+IE K + + GK+VIATVKGDVHDIGKNIVGVVL CN Y++VDL
Sbjct: 725 RVMKQAVAHLIPYIEEEKARTGASSKGKIVIATVKGDVHDIGKNIVGVVLGCNGYDVVDL 784
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVP EKIL AKE A IGLSGLITPSL+EM +VA EM+RQGF +PLLIGGATTS+A
Sbjct: 785 GVMVPTEKILHAAKEHGAQAIGLSGLITPSLEEMSHVASEMQRQGFNVPLLIGGATTSRA 844
Query: 841 HTAVKIEQNYSGPTVYVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKPR 900
HTA+KI NY P VYV +ASR VGVV +LLS+ QR+ + A +Y +R QH KK
Sbjct: 845 HTAIKIAPNYQAPVVYVPDASRAVGVVTSLLSEGQRESYAAEVAADYANIRQQHAGKK-G 903
Query: 901 TPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLAGK 959
+ VTL AR N +D P V +LG+Q + + + TL YIDW PFF TW LAG+
Sbjct: 904 SAMVTLAEARANRLPWD-ATLVPTVPQKLGLQVLQDIDLATLAKYIDWGPFFQTWDLAGR 962
Query: 960 YPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETR 1019
+P IL+D VVG A+ ++ DA ML ++ EK L V GL+PAN VGDDI Y DE R
Sbjct: 963 FPAILDDAVVGETARGVYADAQAMLKQIIEEKWLRAGAVFGLWPANAVGDDIVFYADEQR 1022
Query: 1020 THVINVSHHLRQQTEK-TGFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAFEA 1078
+ + H +RQQ ++ AN CL+D+VAPK SG ADY GAFAVT GL + FEA
Sbjct: 1023 SAPVLTWHGIRQQHKRPEDKANLCLSDYVAPKESGIADYAGAFAVTAGLGIEQKLAEFEA 1082
Query: 1079 QHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPAPG 1138
HDDY IM+K+LADRLAEA AE+LH++VRK WGYA +E LSNE+LI+E Y+GIRPAPG
Sbjct: 1083 AHDDYKSIMLKSLADRLAEACAEWLHQKVRKEDWGYAADEQLSNEQLIKEEYRGIRPAPG 1142
Query: 1139 YPACPEHTEKATIWELLEVEKHTGMKLTESFAMWPGASVSGWYFSHPDSKYYAVAQIQRD 1198
YPACP+HT K +++LL+ E + GM LTES+AM P A+VSG++ +HP ++Y+A+ +I +D
Sbjct: 1143 YPACPDHTAKGGLFQLLQPEANIGMGLTESYAMTPAAAVSGFFLAHPQAQYFAIQKIGQD 1202
Query: 1199 QVEDYARRKGMSVTEVERWLAPNL 1222
Q+ED+A R G ++ + +RWLAPNL
Sbjct: 1203 QLEDWASRAGFTLEQAKRWLAPNL 1226
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: 3690
Number of extensions: 162
Number of successful extensions: 8
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: 1226
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1179
Effective search space: 1391220
Effective search space used: 1391220
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 Dsui_0779 Dsui_0779 (5-methyltetrahydrofolate--homocysteine methyltransferase)
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.32350.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 1748.0 0.0 0 1747.8 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_0779 Dsui_0779 5-methyltetrahydrofola
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0779 Dsui_0779 5-methyltetrahydrofolate--homocysteine methyltransferase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1747.8 0.0 0 0 1 1182 [] 13 1196 .. 13 1196 .. 0.97
Alignments for each domain:
== domain 1 score: 1747.8 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfeaGaDivetntFns 74
l++r+l+lDGamGt++q++ Lte+d+rg +ad+a +lkGnndlL lt+Pevi+ ih +y+ aGaDi+etntFn+
lcl|FitnessBrowser__PS:Dsui_0779 13 LQQRLLILDGAMGTMIQRHGLTEKDYRGTrFADHAHDLKGNNDLLLLTRPEVIRGIHAEYLAAGADILETNTFNA 87
689************************************************************************ PP
TIGR02082 75 teialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGPtnklatlspdverpefrnvtydelvd 148
t++++adY+le+ +yeln ++a+larev+deft ++p k+RfvaG+lGPt+++a++spdv++p++rnvt+delv+
lcl|FitnessBrowser__PS:Dsui_0779 88 TKVSQADYKLEAIVYELNVAGARLAREVCDEFTaKNPAKPRFVAGVLGPTSRTASISPDVNDPGYRNVTFDELVE 162
*************************************************************************** PP
TIGR02082 149 aYkeqvkglldGGvDllLietvfDtlnakaalfaveevfeekgrelPilisgvivdksGrtLsGqtleaflasle 223
Y e+++gl dGG+D+lL+etvfDtlnakaalfa+e+ f++ gr+ P++isg+i+d+sGrtLsGqt eaf +sl+
lcl|FitnessBrowser__PS:Dsui_0779 163 NYLEAIRGLTDGGADILLVETVFDTLNAKAALFAIETFFDKVGRRWPVMISGTITDASGRTLSGQTAEAFWNSLN 237
*************************************************************************** PP
TIGR02082 224 haeililGLnCalGadelrefvkelsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCC 298
h l++GLnCalGa+elr++v+els+ +++vs++PnaGLPna+g Yd+tpe+la++++++a++g++nivGGCC
lcl|FitnessBrowser__PS:Dsui_0779 238 HIRPLSFGLNCALGAKELRQYVEELSRVCDCFVSAHPNAGLPNAFGGYDETPEQLAEEIADWARHGFVNIVGGCC 312
*************************************************************************** PP
TIGR02082 299 GttPehiraiaeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeealki 373
Gt P+hi+aia++v++i+pr +++e++++lsgle+++++++s +vn+GeRtnv+Gsk f+++i ++ y++al +
lcl|FitnessBrowser__PS:Dsui_0779 313 GTSPDHIAAIAKMVAGIAPRAIPAIEPQLRLSGLEPFNVGPDSLYVNVGERTNVTGSKAFARMILEGRYDDALAV 387
*************************************************************************** PP
TIGR02082 374 akqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGLkviqGkaivnsislkd 448
a+qqve+Gaq++Din+De++lD++a+m+k+l+l+asepdi++vP+mlDss++ev+e+GLk+iqGk+ivnsis+k+
lcl|FitnessBrowser__PS:Dsui_0779 388 ARQQVENGAQVIDINMDEAMLDSVAAMEKFLKLIASEPDISRVPIMLDSSKWEVIETGLKCIQGKGIVNSISMKE 462
*************************************************************************** PP
TIGR02082 449 GeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRayklltekvgfppediifDpniltiatGieehd 523
Ge++Fle+akl+++yGaav+vmafDe+Gqa+t+++k ei+kRay+ll+ +gfp++diifDpni++iatGieehd
lcl|FitnessBrowser__PS:Dsui_0779 463 GEAKFLEQAKLARRYGAAVIVMAFDEKGQADTYARKTEICKRAYDLLVG-IGFPAQDIIFDPNIFAIATGIEEHD 536
************************************************9.************************* PP
TIGR02082 524 ryaidfieaireikeelPdakisgGvsnvsFslrgndavRealhsvFLyeaikaGlDmgivnagklavyddidke 598
+ya+dfi+a+r+i+e+lP+a+isgGvsnvsFs+rgnd+vRea+h+vFLy+ai+aG+ mgivnag+l vydd+++e
lcl|FitnessBrowser__PS:Dsui_0779 537 NYAVDFINATRWIRENLPHAQISGGVSNVSFSFRGNDPVREAIHTVFLYHAIQAGMTMGIVNAGMLGVYDDLEPE 611
*************************************************************************** PP
TIGR02082 599 lrevvedlildrrreatekLlelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleear... 670
lr++ved++l+r++ a e L+e+a++ k+ k+k++ wr lpve+RLe+alvkG++e++ +d+ee r
lcl|FitnessBrowser__PS:Dsui_0779 612 LRQKVEDVVLNRHPGAGEALVEFAQTVKEGKAKDTG--PDLTWRTLPVEKRLEHALVKGITEFVVADTEEVRaal 684
**************************9999999554..7789****************************98555 PP
TIGR02082 671 .kklkapleiiegpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed..kskGkivlatvk 742
k+pl++iegpL++Gm++vGdLFG+GkmfLPqvvksarvmk+ava+L+Py+e+ek+ + +skGkiv+atvk
lcl|FitnessBrowser__PS:Dsui_0779 685 aAAGKPPLAVIEGPLMNGMNTVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPYIEEEKARTgaSSKGKIVIATVK 759
445688****************************************************998889*********** PP
TIGR02082 743 GDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemvevaeemerrgvkiPl 817
GDvhDiGkniv+vvL+cngy+vvdlGv+vP+ekil+aak++ a iglsGLi++sl+em +va em+r+g+++Pl
lcl|FitnessBrowser__PS:Dsui_0779 760 GDVHDIGKNIVGVVLGCNGYDVVDLGVMVPTEKILHAAKEHGAQAIGLSGLITPSLEEMSHVASEMQRQGFNVPL 834
*************************************************************************** PP
TIGR02082 818 llGGaalskahvavkiaekYkgevvyvkdaseavkvvdkllsekkkaeelekikeeyeeirekfgekkeklials 892
l+GGa++s+ah+a kia++Y+++vvyv das+av vv +llse +++++++++ ++y +ir+++ k+ ++
lcl|FitnessBrowser__PS:Dsui_0779 835 LIGGATTSRAHTAIKIAPNYQAPVVYVPDASRAVGVVTSLLSEGQRESYAAEVAADYANIRQQHAG-KKGSAMVT 908
****************************************************************98.55677889 PP
TIGR02082 893 ekaarkevfaldrsedlevpapkflGtkvleas.ieellkyiDwkalFvqWelrgkypkilkdeleglearklfk 966
+++ar +++ d + l +++p++lG +vl+++ +++l kyiDw ++F +W+l+g++p il+d ++g+ ar +++
lcl|FitnessBrowser__PS:Dsui_0779 909 LAEARANRLPWDAT--LVPTVPQKLGLQVLQDIdLATLAKYIDWGPFFQTWDLAGRFPAILDDAVVGETARGVYA 981
99999887766655..*********************************************************** PP
TIGR02082 967 dakelldklsaekllrargvvGlfPaqsvgddieiytdetvsqetkpiatvrek.leqlrqqsdrylclaDfias 1040
da+++l+++++ek lra +v+Gl+Pa+ vgddi+ y+de++ p+ t + +++ r + + +lcl+D++a+
lcl|FitnessBrowser__PS:Dsui_0779 982 DAQAMLKQIIEEKWLRAGAVFGLWPANAVGDDIVFYADEQR---SAPVLTWHGIrQQHKRPEDKANLCLSDYVAP 1053
*************************************9999...3444444444044444444459********* PP
TIGR02082 1041 kesGikDylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeeenldked 1115
kesGi+Dy ga++vtaglg+e+ ++ea +ddy+si++k+ladrlaea ae+lh++vRke wgya++e+l++e+
lcl|FitnessBrowser__PS:Dsui_0779 1054 KESGIADYAGAFAVTAGLGIEQKLAEFEAAHDDYKSIMLKSLADRLAEACAEWLHQKVRKEDWGYAADEQLSNEQ 1128
*************************************************************************** PP
TIGR02082 1116 llkerYrGirpafGYpacPdhtekatlleLleaer.iGlklteslalaPeasvsglyfahpeakYfav 1182
l+ke+YrGirpa+GYpacPdht k l++Ll++e iG+ ltes+a++P+a+vsg+++ahp+a+Yfa+
lcl|FitnessBrowser__PS:Dsui_0779 1129 LIKEEYRGIRPAPGYPACPDHTAKGGLFQLLQPEAnIGMGLTESYAMTPAAAVSGFFLAHPQAQYFAI 1196
**********************************99******************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1226 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: 0.07u 0.04s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 13.77
//
[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