Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_035239932.1 Q366_RS13685 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000745975.1:WP_035239932.1
Length = 758
Score = 838 bits (2166), Expect = 0.0
Identities = 437/756 (57%), Positives = 533/756 (70%), Gaps = 16/756 (2%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LGFPR+G RELK A ESYW G +++ +LL G LR +W QK +D +PVGDF+
Sbjct: 4 HNLGFPRIGDNRELKHALESYWRGETSQNQLLETGARLRKNNWAGQK--ALDYVPVGDFS 61
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGR-APTGEP--AAAAEMTKWFNTN 122
+YDHVL TS +LGN+PAR + GS +D FR RG+ A GE A EMTKWF+TN
Sbjct: 62 FYDHVLDTSWMLGNIPARARETCGS-PLDRYFRTARGQSAGDGEANQICAGEMTKWFDTN 120
Query: 123 YHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFDRLS 182
YHY+VPEF F L LLD++ EA G KPV+LGPVT+L+LGK E D+ +
Sbjct: 121 YHYIVPEFDPSSGFCLDAQPLLDQIQEAQKSGVTPKPVILGPVTYLFLGKA--ENIDKKT 178
Query: 183 LLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQ-VKLLLT 241
LL +LP Y ++L LA R +EWVQ+DEP +V +L W + AY L + VK++L
Sbjct: 179 LLKKLLPEYARLLNLLADRDVEWVQMDEPLMVTDLDNDWKLLVEQAYQTLGNEAVKIMLA 238
Query: 242 TYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWRADL 301
TYF + NLD +LPVQ LHVD V GKD V +L RLP LS G+I+GRN+W+ DL
Sbjct: 239 TYFGSLGDNLDLALSLPVQALHVDAVRGKDQVPDLVSRLPEHMALSLGVIDGRNIWKTDL 298
Query: 302 T---EKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHELAL 358
++ A I D +G R LW+A SC+LLH P+DL ET LD E+ SW AFA QK EL L
Sbjct: 299 NALLDQLAPIHDQLGDR-LWLAPSCALLHVPVDLEKETGLDTELLSWMAFARQKLVELDL 357
Query: 359 LRDALNSGDT---AALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYEVRAE 415
L ALN G T AAL E + ++ R++S R+HNP V+ RLA + QR Y RA+
Sbjct: 358 LATALNQGRTLVAAALEENAKALENRKNSARIHNPEVQARLARVDDSWGQRNQPYPERAK 417
Query: 416 AQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVEQERL 475
+ R LP +PTTTIGSFPQT EIR LRL FKKG + + Y GI + I+ I QE +
Sbjct: 418 IHKERLNLPLYPTTTIGSFPQTKEIRALRLKFKKGEISQDAYTAGIRDQIRTTIEFQEEI 477
Query: 476 GLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAPITVE 535
GLDVLVHGEAERNDMVEYFGE LDGF F++ GWVQSYGSRCVKPPI+ GD+SRP P+TV
Sbjct: 478 GLDVLVHGEAERNDMVEYFGEQLDGFAFSRYGWVQSYGSRCVKPPILFGDVSRPRPMTVA 537
Query: 536 WAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAAGIGI 595
W YAQSL++KPVKGMLTGPVTIL WSF R+D SR +QIALA+RDEV DLE AG+ I
Sbjct: 538 WIGYAQSLSEKPVKGMLTGPVTILNWSFVRDDQSRADTCRQIALAIRDEVLDLEKAGVSI 597
Query: 596 IQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIMDSIA 655
IQ+DE ALREGLPLR+ W AYL W V AFRI A KD TQ+HTHMCY EFNDI+D+I
Sbjct: 598 IQLDEAALREGLPLRKHQWKAYLNWAVGAFRIAANGVKDATQLHTHMCYSEFNDIIDAIT 657
Query: 656 ALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKAAKRI 715
+DADVITIE SRS+ME+L +F++ YPNEIGPGVYDIHSPNVPSVE+I A +++AAKRI
Sbjct: 658 RMDADVITIEASRSNMEILNAFDKTAYPNEIGPGVYDIHSPNVPSVEFIVANMQEAAKRI 717
Query: 716 PAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
P ERLW+NPDCGLKTR WPET+A+L N+ AA+ LR
Sbjct: 718 PKERLWINPDCGLKTRAWPETKASLKNLAAAAKELR 753
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: 1607
Number of extensions: 75
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: 753
Length of database: 758
Length adjustment: 40
Effective length of query: 713
Effective length of database: 718
Effective search space: 511934
Effective search space used: 511934
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 WP_035239932.1 Q366_RS13685 (5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase)
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.26860.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 1094.9 0.0 0 1094.7 0.0 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035239932.1 Q366_RS13685 5-methyltetrahydrop
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035239932.1 Q366_RS13685 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltr
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1094.7 0.0 0 0 1 753 [. 6 754 .. 6 755 .. 0.99
Alignments for each domain:
== domain 1 score: 1094.7 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig +Relk+ale+yw+g++s+++ll++ + lrk++++ qk +d++pv+dfs+YDhvLdt+ +
lcl|NCBI__GCF_000745975.1:WP_035239932.1 6 LGFPRIGDNRELKHALESYWRGETSQNQLLETGARLRKNNWAGQK--ALDYVPVGDFSFYDHVLDTSWM 72
79****************************************999..58******************** PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek.....kdvaalemtkwfntnYhYlvPelskeeefklskn 133
lg+ip+r +e+ ++ ld+yF++aRG++ +++ a emtkwf+tnYhY+vPe+++++ f l+++
lcl|NCBI__GCF_000745975.1:WP_035239932.1 73 LGNIPARARETCGS--PLDRYFRTARGQSAgdgeaNQICAGEMTKWFDTNYHYIVPEFDPSSGFCLDAQ 139
**********9555..5**********988899988999****************************** PP
TIGR01371 134 klleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqid 202
ll++++ea++ gv kPv+lGp+t+l+L+ka++ ++++ll+kllp Y ++l+ la+++vewvq+d
lcl|NCBI__GCF_000745975.1:WP_035239932.1 140 PLLDQIQEAQKSGVTPKPVILGPVTYLFLGKAEN---IDKKTLLKKLLPEYARLLNLLADRDVEWVQMD 205
******************************9995...7899**************************** PP
TIGR01371 203 ePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelel 271
eP++v+dl+++++ +v++ay++l + +++k++l+tYf+s+ ++l+ ++slpv+al++D v++k++
lcl|NCBI__GCF_000745975.1:WP_035239932.1 206 EPLMVTDLDNDWKLLVEQAYQTLGN--EAVKIMLATYFGSLGDNLDLALSLPVQALHVDAVRGKDQVPD 272
************************8..699************************************999 PP
TIGR01371 272 akakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkel 340
+++++e+ L++GvidGrniwk+dl++ l++l+ ++++ gd+l++++sc+llhvpvdle+e+ ld+el
lcl|NCBI__GCF_000745975.1:WP_035239932.1 273 LVSRLPEHMALSLGVIDGRNIWKTDLNALLDQLAPIHDQLGDRLWLAPSCALLHVPVDLEKETGLDTEL 341
********************************************************************* PP
TIGR01371 341 kellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarres 408
+++afa++kl el++l++al++ ++ va+ale++a+a+++rk+s+r+++ +v++rl+ ++++ +r++
lcl|NCBI__GCF_000745975.1:WP_035239932.1 342 LSWMAFARQKLVELDLLATALNQgRTLVAAALEENAKALENRKNSARIHNPEVQARLARVDDSWGQRNQ 410
***********************999******************************************* PP
TIGR01371 409 sfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelgl 477
++ eRa++ +++lnlPl+PtttiGsfPqtke+R R kf+kgeis+++Y++ i+++i+ +i++qee+gl
lcl|NCBI__GCF_000745975.1:WP_035239932.1 411 PYPERAKIHKERLNLPLYPTTTIGSFPQTKEIRALRLKFKKGEISQDAYTAGIRDQIRTTIEFQEEIGL 479
********************************************************************* PP
TIGR01371 478 DvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltsk 546
DvLvhGe+eRnDmveyFge+l+Gfaf ++gWvqsYGsRcvkPpi++gdvsrp+pmtv+++ yaqsl++k
lcl|NCBI__GCF_000745975.1:WP_035239932.1 480 DVLVHGEAERNDMVEYFGEQLDGFAFSRYGWVQSYGSRCVKPPILFGDVSRPRPMTVAWIGYAQSLSEK 548
********************************************************************* PP
TIGR01371 547 pvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdke 615
pvkGmLtGPvtilnWsfvR+D++r+++++qiala+rdev dLe+ag++iiq+De+alReglPlrk++++
lcl|NCBI__GCF_000745975.1:WP_035239932.1 549 PVKGMLTGPVTILNWSFVRDDQSRADTCRQIALAIRDEVLDLEKAGVSIIQLDEAALREGLPLRKHQWK 617
********************************************************************* PP
TIGR01371 616 eYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkye 684
+Yl+wav aFr+aa+gvkd+tq+hthmCYsefn+ii+ai+ +daDvi+ieasrs+me+l+a+++ ++y+
lcl|NCBI__GCF_000745975.1:WP_035239932.1 618 AYLNWAVGAFRIAANGVKDATQLHTHMCYSEFNDIIDAITRMDADVITIEASRSNMEILNAFDK-TAYP 685
****************************************************************.67** PP
TIGR01371 685 keiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRe 753
+eiG+GvyDihsp+vPs+e + + +++a k++pkerlW+nPDCGLktR+w+e+ka+lknl +aakelR+
lcl|NCBI__GCF_000745975.1:WP_035239932.1 686 NEIGPGVYDIHSPNVPSVEFIVANMQEAAKRIPKERLWINPDCGLKTRAWPETKASLKNLAAAAKELRA 754
*******************************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (758 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: 00:00:00.05
# Mc/sec: 9.71
//
[ok]
This GapMind analysis is from Apr 10 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