Align methionine synthase; EC 2.1.1.13 (characterized)
to candidate Pf6N2E2_2068 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
Query= CharProtDB::CH_090726
(1227 letters)
>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068
Length = 1236
Score = 1610 bits (4168), Expect = 0.0
Identities = 825/1236 (66%), Positives = 977/1236 (79%), Gaps = 17/1236 (1%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
S+++ L+ L ERIL+LDGGMGTMIQSY+L E D+RG+RFADWP D+KGNNDLLVLS+P
Sbjct: 5 SARLYLLQQALKERILILDGGMGTMIQSYKLEEQDYRGKRFADWPSDVKGNNDLLVLSRP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+VI AI AY +AGADI+ETNTFN+T ++ ADY M+ L+ E+N A+LAR AD T
Sbjct: 65 DVIGAIEKAYLDAGADILETNTFNATQVSQADYGMQGLAYELNLEGARLARKVADAKTLE 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
TPEKPR+VAGVLGPT+RT S+SPDVN+P +RN+TFD LV Y E+TK L+EGG DLILIE
Sbjct: 125 TPEKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGCDLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FAV+ +EALGVELPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185 TIFDTLNAKAAIFAVQGVYEALGVELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPI 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYD-LDADTMAKQIREWAQ 300
+ GLNCALG ELR Y++ELS A +V+AHPNAGLPN FGEYD L A+T AK I E+AQ
Sbjct: 245 SVGLNCALGASELRPYLEELSNKANTHVSAHPNAGLPNEFGEYDELPAET-AKVIEEFAQ 303
Query: 301 AGFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVG 360
+GFLNIVGGCCGTTP HI A+++AV G APR +PEIP ACRLSGLEP I SLFVNVG
Sbjct: 304 SGFLNIVGGCCGTTPAHIEAIAKAVAGYAPRPIPEIPRACRLSGLEPFTIDRSSLFVNVG 363
Query: 361 ERTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLI 420
ERTN+TGSAKF RLI+E+ Y+EAL+VA QQVE GAQ+IDINMDEGMLD++ AMV FLNLI
Sbjct: 364 ERTNITGSAKFARLIREDNYTEALEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLI 423
Query: 421 AGEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAV 480
AGEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ FIHHAKL +RYGAAV
Sbjct: 424 AGEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAV 483
Query: 481 VVMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQ 540
VVMAFDE GQADT ARK EIC+R+Y IL EVGFPPEDIIFDPNIFAVATGIEEHNNYA
Sbjct: 484 VVMAFDEAGQADTEARKKEICKRSYDILVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAV 543
Query: 541 DFIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAG 600
DFI AC I+ ELP+AL SGGVSNVSFSFRGN+PVREAIH+VFL YAIR G+ MGIVNAG
Sbjct: 544 DFINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRAGLTMGIVNAG 603
Query: 601 QLAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVN 660
QL IYD +P ELRDAVEDVILNR +GT+ LL +A+KY+G A+ EWR WEVN
Sbjct: 604 QLEIYDQIPVELRDAVEDVILNRTPEGTDALLAIADKYKGD--GSVKEAETEEWRGWEVN 661
Query: 661 KRLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVK 720
KRLE++LVKGIT I +DTEE+R RPIEVIEGPLM GMN+VGDLFG GKMFLPQVVK
Sbjct: 662 KRLEHALVKGITTHIVEDTEESRLSFARPIEVIEGPLMAGMNIVGDLFGAGKMFLPQVVK 721
Query: 721 SARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVD 779
SARVMKQAVA+L PFIEA K ++ + GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVD
Sbjct: 722 SARVMKQAVAHLIPFIEAEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVD 781
Query: 780 LGVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSK 839
LGVMVPAEKIL+ AKE D+IGLSGLITPSLDEMV+VA+EM+RQ F +PL+IGGATTSK
Sbjct: 782 LGVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVHVAREMQRQDFHLPLMIGGATTSK 841
Query: 840 AHTAVKIEQNYSGPTV-YVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKK 898
AHTAVKIE YS V YV +ASR VGV LLS + FV +TR +Y VR + +
Sbjct: 842 AHTAVKIEPKYSNDAVIYVTDASRAVGVATQLLSKELKPAFVEKTRLDYMDVRERTSNRS 901
Query: 899 PRTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEV-EASIETLRNYIDWTPFFMTWSLA 957
RT ++ AA FDW +Y P G + + + + L YIDWTPFF++W LA
Sbjct: 902 ARTERLSYAAAIAKKPQFDWSSYQPVKPTFTGARVLDDIDLNVLAEYIDWTPFFISWDLA 961
Query: 958 GKYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRD 1016
GKYPRIL DEVVG A L+ DA ML KL EK ++ R V G +PAN+V DD+E+Y D
Sbjct: 962 GKYPRILTDEVVGEAATALYADARAMLRKLIDEKLISARAVFGFWPANQVHDDDLEVYGD 1021
Query: 1017 ETRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADA 1075
+ + + HHLRQQ KT G N+ LADFVAPK SG DY+G F T G+ + +A A
Sbjct: 1022 DGKP--LARLHHLRQQIIKTDGKPNFSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKA 1079
Query: 1076 FEAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRP 1135
++ DDYN IMVKALADRLAEA AE+LH++VRK YWGYA +E+L N+ LI+E Y GIRP
Sbjct: 1080 YQEAGDDYNSIMVKALADRLAEACAEWLHQQVRKNYWGYAQDESLDNDALIKEQYTGIRP 1139
Query: 1136 APGYPACPEHTEKATIWELLEVEK------HTGMKLTESFAMWPGASVSGWYFSHPDSKY 1189
APGYPACP+HTEKAT++ LL+ E +G+ LTE +AM+P A+VSGWYF+HP ++Y
Sbjct: 1140 APGYPACPDHTEKATLFRLLDPEASELKAGRSGVFLTEHYAMFPAAAVSGWYFAHPQAQY 1199
Query: 1190 YAVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
+AV +I +DQV+ Y RKG ++ ERWL+PNLGYD
Sbjct: 1200 FAVGKIDKDQVQSYTARKGQELSVTERWLSPNLGYD 1235
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: 3798
Number of extensions: 176
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: 1236
Length adjustment: 47
Effective length of query: 1180
Effective length of database: 1189
Effective search space: 1403020
Effective search space used: 1403020
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 Pf6N2E2_2068 (5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13))
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.21989.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 1753.9 0.0 0 1753.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 5-methyltetrahydrofolate--homocy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1753.7 0.0 0 0 1 1182 [] 15 1202 .. 15 1202 .. 0.98
Alignments for each domain:
== domain 1 score: 1753.7 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfe 61
l++ril+lDG+mGt++qs++L+e+d+rg+ +ad+++++kGnndlL+l++P+vi ai +ay++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 15 LKERILILDGGMGTMIQSYKLEEQDYRGKrFADWPSDVKGNNDLLVLSRPDVIGAIEKAYLD 76
579*********************************************************** PP
TIGR02082 62 aGaDivetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGP 122
aGaDi+etntFn+t++++adY+++ +ayeln ++a+lar+vad t tpek+RfvaG+lGP
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 77 AGADILETNTFNATQVSQADYGMQGLAYELNLEGARLARKVADAKTlETPEKPRFVAGVLGP 138
********************************************99899************* PP
TIGR02082 123 tnklatlspdverpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfave 184
t+++ +lspdv++p++rnvt+delv+ Y+e++kgl++GG Dl+Liet+fDtlnakaa+fav+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 139 TSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGCDLILIETIFDTLNAKAAIFAVQ 200
************************************************************** PP
TIGR02082 185 evfeekgrelPilisgvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvk 246
v+e+ g+elPi+isg+i+d+sGrtLsGqt+eaf +s+ ha+ +++GLnCalGa elr++++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 201 GVYEALGVELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPISVGLNCALGASELRPYLE 262
************************************************************** PP
TIGR02082 247 elsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPehirai 308
els++a++ vs++PnaGLPn++geYd++p e+ak+++efa+ g+lnivGGCCGttP+hi ai
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 263 ELSNKANTHVSAHPNAGLPNEFGEYDELPAETAKVIEEFAQSGFLNIVGGCCGTTPAHIEAI 324
************************************************************** PP
TIGR02082 309 aeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeea 370
a+av++ +pr +e++ +++lsgle+++i++ s fvn+GeRtn++Gs+kf++li++++y ea
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 325 AKAVAGYAPRPIPEIPRACRLSGLEPFTIDRSSLFVNVGERTNITGSAKFARLIREDNYTEA 386
************************************************************** PP
TIGR02082 371 lkiakqqveeGaqilDinvDevllDgeadmkkllsllasepdiakvPlmlDssefevleaGL 432
l++a qqve Gaq++Din+De++lD++++m+++l+l+a+epdi++vP+m+Dss++ev+eaGL
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 387 LEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIAGEPDISRVPIMIDSSKWEVIEAGL 448
************************************************************** PP
TIGR02082 433 kviqGkaivnsislkdGeerFlekaklikeyGaavvvmafDeeGqartadkkieiakRaykl 494
k+iqGk+ivnsis+k+G+e+F+++akl k+yGaavvvmafDe Gqa+t ++k ei+kR y++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 449 KCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVVVMAFDEAGQADTEARKKEICKRSYDI 510
************************************************************** PP
TIGR02082 495 ltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFsl 556
l+++vgfppediifDpni+++atGieeh++ya+dfi+a+ i+ elP+a +sgGvsnvsFs+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 511 LVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVDFINACAYIRDELPYALTSGGVSNVSFSF 572
************************************************************** PP
TIGR02082 557 rgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekL 618
rgn++vRea+hsvFL +ai+aGl mgivnag+l++yd+i+ elr++ved+il+r +e t+ L
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 573 RGNNPVREAIHSVFLLYAIRAGLTMGIVNAGQLEIYDQIPVELRDAVEDVILNRTPEGTDAL 634
************************************************************** PP
TIGR02082 619 lelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleii 680
l +a++ykg + kea+++ewr+++v++RLe+alvkG++ +i ed+ee+r +p+e+i
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 635 LAIADKYKGDGSV--KEAETEEWRGWEVNKRLEHALVKGITTHIVEDTEESRLSFARPIEVI 694
*********9998..999******************************************** PP
TIGR02082 681 egpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivlatv 741
egpL++Gm++vGdLFG+GkmfLPqvvksarvmk+ava+L+P++e+ek ++ ++kGki++atv
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 695 EGPLMAGMNIVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIEAEKGDKpEAKGKILMATV 756
***********************************************887689********* PP
TIGR02082 742 kGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemve 803
kGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++ak++k D+iglsGLi++sldemv+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 757 KGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVH 818
************************************************************** PP
TIGR02082 804 vaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkka 864
va+em+r+ +++Pl++GGa++skah+avki++kY+ v+yv+das+av v+ +lls++ k
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 819 VAREMQRQDFHLPLMIGGATTSKAHTAVKIEPKYSNdAVIYVTDASRAVGVATQLLSKELKP 880
**********************************872599********************** PP
TIGR02082 865 eelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas. 925
+++ek++ +y ++re+ +++ +++ ls +aa ++ ++d+s +++++p+f G +vl+++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 881 AFVEKTRLDYMDVRERTSNRSARTERLSYAAAIAKKPQFDWS-SYQPVKPTFTGARVLDDId 941
******************************************.9****************** PP
TIGR02082 926 ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvv 987
++ l +yiDw+++F++W+l+gkyp+il+de++g+ a+ l++da+++l kl+ ekl+ ar+v+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 942 LNVLAEYIDWTPFFISWDLAGKYPRILTDEVVGEAATALYADARAMLRKLIDEKLISARAVF 1003
************************************************************** PP
TIGR02082 988 GlfPaqsv.gddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikD 1047
G++Pa++v +dd+e+y d++ p+a +++ ++q+ + ++ + +laDf+a+k+sG +D
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 1004 GFWPANQVhDDDLEVYGDDGK-----PLARLHHLRQQIIKTDGKpNFSLADFVAPKDSGVTD 1060
*****9761578*****8876.....8888888888888888878***************** PP
TIGR02082 1048 ylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeee 1109
y+g +++tag+gaee ak++++ ddy+si+vkaladrlaea ae+lh++vRk++wgya++e
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 1061 YVGGFITTAGIGAEEVAKAYQEAGDDYNSIMVKALADRLAEACAEWLHQQVRKNYWGYAQDE 1122
************************************************************** PP
TIGR02082 1110 nldkedllkerYrGirpafGYpacPdhtekatlleLleae.......riGlklteslalaPe 1164
+ld++ l+ke+Y Girpa+GYpacPdhtekatl++Ll++e r G+ lte +a+ P+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 1123 SLDNDALIKEQYTGIRPAPGYPACPDHTEKATLFRLLDPEaselkagRSGVFLTEHYAMFPA 1184
*************************************9875545444579************ PP
TIGR02082 1165 asvsglyfahpeakYfav 1182
a+vsg+yfahp+a+Yfav
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2068 1185 AAVSGWYFAHPQAQYFAV 1202
****************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (1182 nodes)
Target sequences: 1 (1236 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: 00:00:00.11
# Mc/sec: 13.03
//
[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