Align methionine synthase (EC 2.1.1.13) (characterized)
to candidate Pf1N1B4_5661 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
Query= BRENDA::P13009
(1227 letters)
>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661
5-methyltetrahydrofolate--homocysteine methyltransferase
(EC 2.1.1.13)
Length = 1236
Score = 1615 bits (4183), Expect = 0.0
Identities = 824/1235 (66%), Positives = 978/1235 (79%), Gaps = 15/1235 (1%)
Query: 2 SSKVEQLRAQLNERILVLDGGMGTMIQSYRLNEADFRGERFADWPCDLKGNNDLLVLSKP 61
S +++ L+ L ERIL+LDGGMGTMIQSY+L E D+RG+RFADWP D+KGNNDLLVL++P
Sbjct: 5 SVRLQALKHALKERILILDGGMGTMIQSYKLEEQDYRGKRFADWPSDVKGNNDLLVLTRP 64
Query: 62 EVIAAIHNAYFEAGADIIETNTFNSTTIAMADYQMESLSAEINFAAAKLARACADEWTAR 121
+VI I AY +AGADI+ETNTFN+T I+MADY ME L+ E+N A+LAR AD T
Sbjct: 65 DVIGGIEKAYLDAGADILETNTFNATRISMADYGMEELAYELNVEGARLARKIADAKTLE 124
Query: 122 TPEKPRYVAGVLGPTNRTASISPDVNDPAFRNITFDGLVAAYRESTKALVEGGADLILIE 181
P+KPR+VAGVLGPT+RT S+SPDVN+P +RN+TFD LV Y E+TK L+EGGADLILIE
Sbjct: 125 NPDKPRFVAGVLGPTSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIE 184
Query: 182 TVFDTLNAKAAVFAVKTEFEALGVELPIMISGTITDASGRTLSGQTTEAFYNSLRHAEAL 241
T+FDTLNAKAA+FAV+ FE LGVELPIMISGTITDASGRTLSGQTTEAF+NS+ HA+ +
Sbjct: 185 TIFDTLNAKAAIFAVQGVFEELGVELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPI 244
Query: 242 TFGLNCALGPDELRQYVQELSRIAECYVTAHPNAGLPNAFGEYDLDADTMAKQIREWAQA 301
+ GLNCALG ELR Y++ELS A +V+AHPNAGLPN FGEYD AK I E+AQ+
Sbjct: 245 SVGLNCALGASELRPYLEELSNKANTHVSAHPNAGLPNEFGEYDELPAQTAKVIEEFAQS 304
Query: 302 GFLNIVGGCCGTTPQHIAAMSRAVEGLAPRKLPEIPVACRLSGLEPLNIGEDSLFVNVGE 361
GFLNIVGGCCGTTP HI A+++AV G APR++P+IP ACRLSGLEP I SLFVNVGE
Sbjct: 305 GFLNIVGGCCGTTPGHIEAIAKAVAGYAPREIPDIPKACRLSGLEPFTIDRSSLFVNVGE 364
Query: 362 RTNVTGSAKFKRLIKEEKYSEALDVARQQVENGAQIIDINMDEGMLDAEAAMVRFLNLIA 421
RTN+TGSAKF RLI+E+ Y+EAL+VA QQVE GAQ+IDINMDEGMLD++ AMV FLNLIA
Sbjct: 365 RTNITGSAKFARLIREDNYTEALEVALQQVEAGAQVIDINMDEGMLDSKKAMVTFLNLIA 424
Query: 422 GEPDIARVPIMIDSSKWDVIEKGLKCIQGKGIVNSISMKEGVDAFIHHAKLLRRYGAAVV 481
GEPDI+RVPIMIDSSKW+VIE GLKCIQGKGIVNSISMKEGV+ FIHHAKL +RYGAAVV
Sbjct: 425 GEPDISRVPIMIDSSKWEVIEAGLKCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVV 484
Query: 482 VMAFDEQGQADTRARKIEICRRAYKILTEEVGFPPEDIIFDPNIFAVATGIEEHNNYAQD 541
VMAFDE GQADT ARK EIC+R+Y IL EVGFPPEDIIFDPNIFAVATGIEEHNNYA D
Sbjct: 485 VMAFDEAGQADTEARKKEICKRSYDILVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVD 544
Query: 542 FIGACEDIKRELPHALISGGVSNVSFSFRGNDPVREAIHAVFLYYAIRNGMDMGIVNAGQ 601
FI AC I+ ELP+AL SGGVSNVSFSFRGN+PVREAIH+VFL YAIRNG+ MGIVNAGQ
Sbjct: 545 FINACAYIRDELPYALTSGGVSNVSFSFRGNNPVREAIHSVFLLYAIRNGLTMGIVNAGQ 604
Query: 602 LAIYDDLPAELRDAVEDVILNRRDDGTERLLELAEKYRGSKTDDTANAQQAEWRSWEVNK 661
L IYD +PAELRDAVEDVILNR +GT+ LL +A+KY+G A+ EWR+W+VNK
Sbjct: 605 LEIYDQIPAELRDAVEDVILNRTPEGTDALLAIADKYKGD--GSVKEAETEEWRNWDVNK 662
Query: 662 RLEYSLVKGITEFIEQDTEEARQQATRPIEVIEGPLMDGMNVVGDLFGEGKMFLPQVVKS 721
RLE++LVKGIT I +DTEE+RQ RPIEVIEGPLM GMN+VGDLFG GKMFLPQVVKS
Sbjct: 663 RLEHALVKGITTHIVEDTEESRQSFARPIEVIEGPLMSGMNIVGDLFGAGKMFLPQVVKS 722
Query: 722 ARVMKQAVAYLEPFIEASK-EQGKTNGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDL 780
ARVMKQAVA+L PFIE K ++ + GK+++ATVKGDVHDIGKNIVGVVL CN Y+IVDL
Sbjct: 723 ARVMKQAVAHLIPFIELEKGDKPEAKGKILMATVKGDVHDIGKNIVGVVLGCNGYDIVDL 782
Query: 781 GVMVPAEKILRTAKEVNADLIGLSGLITPSLDEMVNVAKEMERQGFTIPLLIGGATTSKA 840
GVMVPAEKIL+ AKE D+IGLSGLITPSLDEMV+VA+EM+RQ F +PL+IGGATTSKA
Sbjct: 783 GVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVHVAREMQRQDFHLPLMIGGATTSKA 842
Query: 841 HTAVKIEQNYSGPTV-YVQNASRTVGVVAALLSDTQRDDFVARTRKEYETVRIQHGRKKP 899
HTAVKIE YS V YV +ASR VGV LLS + FV +TR EY VR + +
Sbjct: 843 HTAVKIEPKYSNDAVIYVTDASRAVGVATQLLSKELKAGFVEKTRLEYIDVRERTANRSA 902
Query: 900 RTPPVTLEAARDNDFAFDWQAYTPPVAHRLGVQEVE-ASIETLRNYIDWTPFFMTWSLAG 958
RT ++ A FDW +Y P G + ++ ++ L YIDWTPFF++W LAG
Sbjct: 903 RTERLSYPVAIAKKPQFDWGSYEPVKPTFTGAKVLDNIDLKVLAEYIDWTPFFISWDLAG 962
Query: 959 KYPRILEDEVVGVEAQRLFKDANDMLDKLSAEKTLNPRGVVGLFPANRV-GDDIEIYRDE 1017
K+PRIL+DEVVG A L+ DA +ML KL EK ++ R V G +PAN+V DDIE+Y D+
Sbjct: 963 KFPRILKDEVVGEAATALYADAQEMLAKLIDEKLISARAVFGFWPANQVRDDDIEVYDDD 1022
Query: 1018 TRTHVINVSHHLRQQTEKT-GFANYCLADFVAPKLSGKADYIGAFAVTGGLEEDALADAF 1076
+ + HHLRQQ KT G N+ LADFVAPK SG DY+G F T G+ + +A A+
Sbjct: 1023 GKP--LAKLHHLRQQIIKTDGKPNFSLADFVAPKDSGVTDYVGGFITTAGIGAEEVAKAY 1080
Query: 1077 EAQHDDYNKIMVKALADRLAEAFAEYLHERVRKVYWGYAPNENLSNEELIRENYQGIRPA 1136
+ DDYN IMVKALADRLAEA AE+LH++VRK YWGYA +E L NE LI+E Y GIRPA
Sbjct: 1081 QDAGDDYNSIMVKALADRLAEACAEWLHQQVRKDYWGYAKDETLDNEALIKEQYTGIRPA 1140
Query: 1137 PGYPACPEHTEKATIWELLEVEK------HTGMKLTESFAMWPGASVSGWYFSHPDSKYY 1190
PGYPACP+HTEKAT+++LL+ E +G+ LTE +AM+P A+VSGWYF+HP ++Y+
Sbjct: 1141 PGYPACPDHTEKATLFKLLDPEAEELKAGRSGVFLTEHYAMFPAAAVSGWYFAHPQAQYF 1200
Query: 1191 AVAQIQRDQVEDYARRKGMSVTEVERWLAPNLGYD 1225
AV +I +DQV+ Y RKG ++ ERWLAPNLGYD
Sbjct: 1201 AVGKIDKDQVQSYTSRKGQELSVTERWLAPNLGYD 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: 3806
Number of extensions: 174
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: 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 Pf1N1B4_5661 (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.29412.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 1760.6 0.0 0 1760.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 5-methyltetrahydrofolate--homocy
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 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 ! 1760.4 0.0 0 0 1 1182 [] 15 1202 .. 15 1202 .. 0.98
Alignments for each domain:
== domain 1 score: 1760.4 bits; conditional E-value: 0
TIGR02082 1 lnkrilvlDGamGtqlqsanLteadFrge.eadlarelkGnndlLnltkPeviaaihrayfe 61
l++ril+lDG+mGt++qs++L+e+d+rg+ +ad+++++kGnndlL+lt+P+vi i +ay++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 15 LKERILILDGGMGTMIQSYKLEEQDYRGKrFADWPSDVKGNNDLLVLTRPDVIGGIEKAYLD 76
579*********************************************************** PP
TIGR02082 62 aGaDivetntFnsteialadYdledkayelnkkaaklarevadeft.ltpekkRfvaGslGP 122
aGaDi+etntFn+t i++adY++e++ayeln ++a+lar++ad t +p+k+RfvaG+lGP
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 77 AGADILETNTFNATRISMADYGMEELAYELNVEGARLARKIADAKTlENPDKPRFVAGVLGP 138
********************************************9989************** PP
TIGR02082 123 tnklatlspdverpefrnvtydelvdaYkeqvkglldGGvDllLietvfDtlnakaalfave 184
t+++ +lspdv++p++rnvt+delv+ Y+e++kgl++GG+Dl+Liet+fDtlnakaa+fav+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 139 TSRTCSLSPDVNNPGYRNVTFDELVENYTEATKGLIEGGADLILIETIFDTLNAKAAIFAVQ 200
************************************************************** PP
TIGR02082 185 evfeekgrelPilisgvivdksGrtLsGqtleaflaslehaeililGLnCalGadelrefvk 246
vfee g+elPi+isg+i+d+sGrtLsGqt+eaf +s+ ha+ +++GLnCalGa elr++++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 201 GVFEELGVELPIMISGTITDASGRTLSGQTTEAFWNSVAHAKPISVGLNCALGASELRPYLE 262
************************************************************** PP
TIGR02082 247 elsetaealvsviPnaGLPnalgeYdltpeelakalkefaeegllnivGGCCGttPehirai 308
els++a++ vs++PnaGLPn++geYd++p ++ak+++efa+ g+lnivGGCCGttP hi ai
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 263 ELSNKANTHVSAHPNAGLPNEFGEYDELPAQTAKVIEEFAQSGFLNIVGGCCGTTPGHIEAI 324
************************************************************** PP
TIGR02082 309 aeavkdikprkrqeleeksvlsglealkiaqessfvniGeRtnvaGskkfrklikaedyeea 370
a+av++ +pr+ ++++++++lsgle+++i++ s fvn+GeRtn++Gs+kf++li++++y ea
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 325 AKAVAGYAPREIPDIPKACRLSGLEPFTIDRSSLFVNVGERTNITGSAKFARLIREDNYTEA 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__pseudo1_N1B4:Pf1N1B4_5661 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__pseudo1_N1B4:Pf1N1B4_5661 449 KCIQGKGIVNSISMKEGVEQFIHHAKLCKRYGAAVVVMAFDEAGQADTEARKKEICKRSYDI 510
************************************************************** PP
TIGR02082 495 ltekvgfppediifDpniltiatGieehdryaidfieaireikeelPdakisgGvsnvsFsl 556
l+++vgfppediifDpni+++atGieeh++ya+dfi+a+ i+ elP+a +sgGvsnvsFs+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 511 LVNEVGFPPEDIIFDPNIFAVATGIEEHNNYAVDFINACAYIRDELPYALTSGGVSNVSFSF 572
************************************************************** PP
TIGR02082 557 rgndavRealhsvFLyeaikaGlDmgivnagklavyddidkelrevvedlildrrreatekL 618
rgn++vRea+hsvFL +ai++Gl mgivnag+l++yd+i++elr++ved+il+r +e t+ L
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 573 RGNNPVREAIHSVFLLYAIRNGLTMGIVNAGQLEIYDQIPAELRDAVEDVILNRTPEGTDAL 634
************************************************************** PP
TIGR02082 619 lelaelykgtkeksskeaqeaewrnlpveeRLeralvkGeregieedleearkklkapleii 680
l +a++ykg + kea+++ewrn++v++RLe+alvkG++ +i ed+ee+r+ +p+e+i
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 635 LAIADKYKGDGSV--KEAETEEWRNWDVNKRLEHALVKGITTHIVEDTEESRQSFARPIEVI 694
*********9998..999******************************************** PP
TIGR02082 681 egpLldGmkvvGdLFGsGkmfLPqvvksarvmkkavayLePylekekeed.kskGkivlatv 741
egpL+ Gm++vGdLFG+GkmfLPqvvksarvmk+ava+L+P++e ek ++ ++kGki++atv
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 695 EGPLMSGMNIVGDLFGAGKMFLPQVVKSARVMKQAVAHLIPFIELEKGDKpEAKGKILMATV 756
**********************************************9877689********* PP
TIGR02082 742 kGDvhDiGknivdvvLscngyevvdlGvkvPvekileaakkkkaDviglsGLivksldemve 803
kGDvhDiGkniv+vvL+cngy++vdlGv+vP+ekil++ak++k D+iglsGLi++sldemv+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 757 KGDVHDIGKNIVGVVLGCNGYDIVDLGVMVPAEKILQVAKEQKCDIIGLSGLITPSLDEMVH 818
************************************************************** PP
TIGR02082 804 vaeemerrgvkiPlllGGaalskahvavkiaekYkg.evvyvkdaseavkvvdkllsekkka 864
va+em+r+ +++Pl++GGa++skah+avki++kY+ v+yv+das+av v+ +lls++ ka
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 819 VAREMQRQDFHLPLMIGGATTSKAHTAVKIEPKYSNdAVIYVTDASRAVGVATQLLSKELKA 880
**********************************872599********************** PP
TIGR02082 865 eelekikeeyeeirekfgekkeklialsekaarkevfaldrsedlevpapkflGtkvleas. 925
++ek++ ey ++re+ ++ +++ ls a ++ ++d+ +e+++p+f G kvl+++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 881 GFVEKTRLEYIDVRERTANRSARTERLSYPVAIAKKPQFDWG-SYEPVKPTFTGAKVLDNId 941
******************************************.9****************** PP
TIGR02082 926 ieellkyiDwkalFvqWelrgkypkilkdeleglearklfkdakelldklsaekllrargvv 987
++ l +yiDw+++F++W+l+gk+p+ilkde++g+ a+ l++da+e+l kl+ ekl+ ar+v+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 942 LKVLAEYIDWTPFFISWDLAGKFPRILKDEVVGEAATALYADAQEMLAKLIDEKLISARAVF 1003
************************************************************** PP
TIGR02082 988 GlfPaqsv.gddieiytdetvsqetkpiatvrekleqlrqqsdr.ylclaDfiaskesGikD 1047
G++Pa++v +ddie+y+d++ p+a +++ ++q+ + ++ + +laDf+a+k+sG +D
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1004 GFWPANQVrDDDIEVYDDDGK-----PLAKLHHLRQQIIKTDGKpNFSLADFVAPKDSGVTD 1060
*****9762578*****8877.....8888888888888888877***************** PP
TIGR02082 1048 ylgallvtaglgaeelakkleakeddydsilvkaladrlaealaellhervRkelwgyaeee 1109
y+g +++tag+gaee ak++++ ddy+si+vkaladrlaea ae+lh++vRk++wgya++e
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1061 YVGGFITTAGIGAEEVAKAYQDAGDDYNSIMVKALADRLAEACAEWLHQQVRKDYWGYAKDE 1122
************************************************************** PP
TIGR02082 1110 nldkedllkerYrGirpafGYpacPdhtekatlleLleae.......riGlklteslalaPe 1164
ld+e l+ke+Y Girpa+GYpacPdhtekatl++Ll++e r G+ lte +a+ P+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 1123 TLDNEALIKEQYTGIRPAPGYPACPDHTEKATLFKLLDPEaeelkagRSGVFLTEHYAMFPA 1184
*************************************9875455444579************ PP
TIGR02082 1165 asvsglyfahpeakYfav 1182
a+vsg+yfahp+a+Yfav
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5661 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 0.03s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 13.39
//
[ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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