Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate 5210558 Shew_2986 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (RefSeq)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__PV4:5210558
Length = 759
Score = 842 bits (2174), Expect = 0.0
Identities = 430/751 (57%), Positives = 541/751 (72%), Gaps = 7/751 (0%)
Query: 7 TLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFAW 66
+LGFPR+G +RELK A E YW G + +L ++ ELR HW Q+ AG+ +PVGDFA+
Sbjct: 8 SLGFPRIGRQRELKFALEKYWRGEIEQTQLQSLASELRRTHWQWQQAAGVKQVPVGDFAF 67
Query: 67 YDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAAAAEMTKWFNTNYHYM 126
YD VLT S + +PARH++ + VD+DTLFR+ RGRAPTGE + AA+M K+FNTNYHY+
Sbjct: 68 YDQVLTLSATINAIPARHRSGE-QVDLDTLFRVARGRAPTGEASRAAQMKKYFNTNYHYI 126
Query: 127 VPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLSLLND 186
VPE GQ+F++ + QL DEV EA +LGH+ KPVLLGPV++L+L K +GE FD+LSLL +
Sbjct: 127 VPELTAGQRFEIAYEQLFDEVAEAKSLGHQPKPVLLGPVSYLYLAKCEGEPFDKLSLLPN 186
Query: 187 ILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQ-VKLLLTTYFE 245
+L YQ +LA A +G+ WVQ+DEP L LEL WL A++PAY L GQ VKLLL +Y+
Sbjct: 187 LLEAYQAILARFADQGVTWVQLDEPILALELDDDWLAAFEPAYKELSGQGVKLLLASYYG 246
Query: 246 GVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADLTEKY 305
V + + I L V GLH+DLV + + L +LS G+INGRNVW ADL
Sbjct: 247 SVAHHHELIKDLVVDGLHLDLVSDAEQLTLFGASLKPTQVLSLGVINGRNVWAADLDILA 306
Query: 306 AQIKDIV---GKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELALLRDA 362
+++ +V G+R +W+A SCSLLH P+DL ET L E+ + +FA QK ELA LR
Sbjct: 307 ERLRGLVADLGER-VWLAPSCSLLHVPVDLESETELAPELANQLSFAKQKLDELAALRTL 365
Query: 363 LNSGDTAALAEWSAPIQARRH-STRVHNPAVEKRLAAITAQDSQRANVYEVRAEAQRARF 421
L + + A A +ARR + NP V+ RL A+T +D R + + R Q+ARF
Sbjct: 366 LLTPQSEAAQAIVARCEARRQVREQAANPEVQARLKALTPEDFNRPSGFGERRLKQQARF 425
Query: 422 KLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERLGLDVLV 481
+LP PTTTIGSFPQT IR LR ++KG L Y + + +I Q +LG+DVLV
Sbjct: 426 RLPLLPTTTIGSFPQTPAIRGLRSRWRKGELTEQAYVAQLEAVTRDSIARQLKLGIDVLV 485
Query: 482 HGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVEWAKYAQ 541
HGEAERNDMVEYFGE LDG FTQ WVQSYGSRCVKPP++ GD+SR P+T+ WA +AQ
Sbjct: 486 HGEAERNDMVEYFGEQLDGVGFTQFAWVQSYGSRCVKPPLIYGDVSRRQPMTLAWASFAQ 545
Query: 542 SLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGIIQIDEP 601
LTD+PVKGMLTGPVTIL WSF RED+ RE IA Q+ALA+RDEVADL+AAGIGIIQIDEP
Sbjct: 546 GLTDRPVKGMLTGPVTILHWSFAREDIGREQIANQLALAIRDEVADLQAAGIGIIQIDEP 605
Query: 602 ALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIAALDADV 661
A REGLPL+ SDW YL W V AF+++AA A+D+TQIHTHMCY EFN +D+IAA+DADV
Sbjct: 606 AFREGLPLKASDWKHYLDWAVAAFKLSAAGAEDETQIHTHMCYSEFNATIDAIAAMDADV 665
Query: 662 ITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRIPAERLW 721
ITIETSRS MELL +FE+F+YPNEIGPGVYDIHSPN+P+VE + AL++KAA +IP +LW
Sbjct: 666 ITIETSRSHMELLNAFEDFEYPNEIGPGVYDIHSPNIPTVEQMVALIEKAATKIPVGQLW 725
Query: 722 VNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
VNPDCGLKTR W E AL NMV+A + LRR
Sbjct: 726 VNPDCGLKTRTWDEVEPALQNMVKATKELRR 756
Lambda K H
0.319 0.135 0.416
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: 1593
Number of extensions: 61
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: 753
Length of database: 759
Length adjustment: 40
Effective length of query: 713
Effective length of database: 719
Effective search space: 512647
Effective search space used: 512647
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)
Align candidate 5210558 Shew_2986 (5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (RefSeq))
to HMM TIGR01371 (metE: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (EC 2.1.1.14))
# 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/TIGR01371.hmm
# target sequence database: /tmp/gapView.18011.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01371 [M=754]
Accession: TIGR01371
Description: met_syn_B12ind: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
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 1051.8 0.0 0 1051.6 0.0 1.0 1 lcl|FitnessBrowser__PV4:5210558 Shew_2986 5-methyltetrahydropter
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210558 Shew_2986 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (Re
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1051.6 0.0 0 0 1 753 [. 9 756 .. 9 757 .. 0.98
Alignments for each domain:
== domain 1 score: 1051.6 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavllgaiperfk 78
lgfPrig++Relk+alekyw+g+i++ +l++ a++lr+++++ q++agv+ +pv+df++YD+vL++++ ++aip+r++
lcl|FitnessBrowser__PV4:5210558 9 LGFPRIGRQRELKFALEKYWRGEIEQTQLQSLASELRRTHWQWQQAAGVKQVPVGDFAFYDQVLTLSATINAIPARHR 86
79***************************************************************************9 PP
TIGR01371 79 eladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPvll 154
+ +++dldt+F++aRG + + + a +m+k+fntnYhY+vPel++ ++f+++ ++l++e+ eak+lg++ kPvll
lcl|FitnessBrowser__PV4:5210558 87 SG--EQVDLDTLFRVARGRAPtgEASRAAQMKKYFNTNYHYIVPELTAGQRFEIAYEQLFDEVAEAKSLGHQPKPVLL 162
96..7789**********98765678899************************************************* PP
TIGR01371 155 GpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeaskel 232
Gp+++l+Lak + +e +++l+ll++ll++Y+ +l ++a++gv+wvq+deP+l+l+l++++laa++ ay+el+ + +
lcl|FitnessBrowser__PV4:5210558 163 GPVSYLYLAKCE-GEPFDKLSLLPNLLEAYQAILARFADQGVTWVQLDEPILALELDDDWLAAFEPAYKELSG--QGV 237
*********999.699********************************************************8..69* PP
TIGR01371 233 klllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleak 310
klll++Y++sv ++ e +++l v++l+lDlv+++e+l+l a+++ +vL++Gvi+Grn+w+adl +++l+ l a
lcl|FitnessBrowser__PV4:5210558 238 KLLLASYYGSVAHHHELIKDLVVDGLHLDLVSDAEQLTLFGASLKPTQVLSLGVINGRNVWAADLDILAERLRGLVAD 315
****************************************************************************** PP
TIGR01371 311 agdklvvstscsllhvpvdleleekldkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrv 387
g+++++++scsllhvpvdle e++l +el + l+fak+kl+el++l+++l ++++a+a+ a+ a+r+ +++
lcl|FitnessBrowser__PV4:5210558 316 LGERVWLAPSCSLLHVPVDLESETELAPELANQLSFAKQKLDELAALRTLLLTpQSEAAQAIVARC--EARRQVREQA 391
***************************************************997888888888763..4456677788 PP
TIGR01371 388 adekvkerlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeei 465
a+ +v++rl+al+ ++++r s f eR+ +q+++++lPllPtttiGsfPqt +R R+++rkge++e++Y++ +++ +
lcl|FitnessBrowser__PV4:5210558 392 ANPEVQARLKALTPEDFNRPSGFGERRLKQQARFRLPLLPTTTIGSFPQTPAIRGLRSRWRKGELTEQAYVAQLEAVT 469
89**************************************************************************** PP
TIGR01371 466 kkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsl 543
++ i+ q +lg+DvLvhGe+eRnDmveyFge+l+G ftq++WvqsYGsRcvkPp+iygdvsr +pmt+++ +aq+l
lcl|FitnessBrowser__PV4:5210558 470 RDSIARQLKLGIDVLVHGEAERNDMVEYFGEQLDGVGFTQFAWVQSYGSRCVKPPLIYGDVSRRQPMTLAWASFAQGL 547
****************************************************************************** PP
TIGR01371 544 tskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldwa 621
t++pvkGmLtGPvtil+Wsf ReD+ r++ia+q+ala+rdev+dL++agi iiqiDepa+ReglPl++sd+++Yldwa
lcl|FitnessBrowser__PV4:5210558 548 TDRPVKGMLTGPVTILHWSFAREDIGREQIANQLALAIRDEVADLQAAGIGIIQIDEPAFREGLPLKASDWKHYLDWA 625
****************************************************************************** PP
TIGR01371 622 veaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGlGvyDihsprv 699
v aF+l+a+g++detqihthmCYsefn i+aiaa+daDvi+ie+srs+mell+a+++ ++y++eiG+GvyDihsp++
lcl|FitnessBrowser__PV4:5210558 626 VAAFKLSAAGAEDETQIHTHMCYSEFNATIDAIAAMDADVITIETSRSHMELLNAFED-FEYPNEIGPGVYDIHSPNI 702
**********************************************************.67***************** PP
TIGR01371 700 PskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
P++e++ +l+eka +k+p +lWvnPDCGLktR w+ev++al+n+v+a+kelR
lcl|FitnessBrowser__PV4:5210558 703 PTVEQMVALIEKAATKIPVGQLWVNPDCGLKTRTWDEVEPALQNMVKATKELRR 756
***************************************************996 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (759 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 12.70
//
[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