Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_011610649.1 TERY_RS04005 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Query= BRENDA::A0A077D1A3
(765 letters)
>NCBI__GCF_000014265.1:WP_011610649.1
Length = 744
Score = 682 bits (1759), Expect = 0.0
Identities = 356/761 (46%), Positives = 497/761 (65%), Gaps = 27/761 (3%)
Query: 6 TATLGLSRMGPNRELKFAMEKYWKGKIGKDEFIAKAQAVEELGWSLQLADDKIDSIPVGE 65
T+TLG R+G NRE+K A+E +W+ KI DE + + +EE W Q I+ I +G+
Sbjct: 5 TSTLGYPRIGKNREVKKALESFWQQKISADELLKIVREIEEASWQTQTKAG-IERIGIGD 63
Query: 66 HFYYDGVLSWAEWLGIVPKRFAHLDAGIDRMFAMARGVDGATALGLKKWFTTNYHYLPSE 125
YD +L W+ GI+PKRF ++ FAMARG DG AL + KWF TNYHYL E
Sbjct: 64 ATLYDQILDWSFRFGIIPKRFQQFQ-NLECYFAMARGKDGILALEMTKWFDTNYHYLVPE 122
Query: 126 VDTKRSP-ANLTDYLANVKRGLQFVGADKARAVIYGPVTIIRHSTFAQTEGSIDVQRFAL 184
+ +P A+ +D+L VKR + +G A +I P+T IR S E +
Sbjct: 123 ITPDITPKADFSDFLETVKRAKKIIGKS-AVPIIISPITFIRLSRLESVEFD------NI 175
Query: 185 LAELIPIYQKLIQDLSDMGVKEIQIHEPALVFDESSKLLPLYKQAYPSILANKKSTTRID 244
LA+L+P+Y L+ L +G+ EIQ+HEPALVF +SS L ++ AY + K I
Sbjct: 176 LAQLLPLYSDLLTKLKKLGISEIQLHEPALVFGDSSNLKKQFEMAYAELA---KVGLNIH 232
Query: 245 MVTYFEDVGADNWTWLMEQSEINKVSLDFTRGDNLALLKSNGFPKEKTLGAGIIDARSPW 304
+VTYF+D+G + + W+M+ + +SLD TRG NL L+KS GFP +KTLGAG++DAR+ W
Sbjct: 233 LVTYFDDLG-ETYPWVMKLP-VTSISLDLTRGQNLELIKSYGFPADKTLGAGVVDARNIW 290
Query: 305 KVDPSKILPLIEELQSLGVSKDRLCIQPCASLQFVPWDLQNGEDNNLLKHQASKVLSFQQ 364
++ ++ L+EEL+ + + +QP ASLQFVP+D++ L VLSF +
Sbjct: 291 RIRTQEVTSLLEELKGI---IPNISVQPSASLQFVPYDVRREVK---LPEALRNVLSFAE 344
Query: 365 QKIDELHALAT-----SDKKFVADTNEAWSVYKSSGTRNEEVGKAVAGLTEKDFTRGETF 419
QK++E L+ S+K + + W + NE+V + L E DF R ++
Sbjct: 345 QKLEETVLLSKALTGKSNKSEIENIEIYWQEFYKFSPANEKVKSQIKALKETDFRRSMSY 404
Query: 420 EVRRPKQMPELPILPTTSIGSFPQTAGIRRLRQQLKKGTMSKEEYEAAIDKEITFMIGIQ 479
R Q+ +LP PTT+IGSFPQT +R+LR + KKG +++ EY A ID I + IG+Q
Sbjct: 405 LERLDNQI-KLPAFPTTTIGSFPQTKQVRKLRARYKKGELTQAEYLAQIDANIAYCIGLQ 463
Query: 480 EGLGLDILVHGEPERTDMVEFFAQQMNGMLFSGNGWVQSFGSRCVRPPIIWADVSLDHAM 539
EG+G+D+LVHGE ER+DMVE+F +Q++G F+ +GWVQS+GSR VRPPII+ D+ HAM
Sbjct: 464 EGMGMDVLVHGEFERSDMVEYFGEQLDGYTFTTHGWVQSYGSRYVRPPIIFGDIYRPHAM 523
Query: 540 TTREFKVAQSLTKKPVKGMLTGPITILNWSFPRADISRKEQTFQIGLALRKEIAYLEEAG 599
T REF+VAQSLT+KPVKGMLTGP+T+LNWS+PR DISR+EQ FQ+ LA+R+E+ LE+AG
Sbjct: 524 TIREFEVAQSLTEKPVKGMLTGPVTMLNWSYPRTDISRQEQAFQLALAIREELKDLEKAG 583
Query: 600 CRVIQVDEPALREGMPMRSARKDEYLRWAVDAFRLATAAAKSETSIHTHMCYCEFGDCME 659
IQVDEPA+REG+P++ R EYL WAVDAFRL+TA A+ ET +HTHMCY EFGD ME
Sbjct: 584 AAFIQVDEPAMREGLPLKQQRWHEYLNWAVDAFRLSTAIARPETQVHTHMCYSEFGDIME 643
Query: 660 ALDEMDADVNSIENARSDDETLRQFKAIGYKKGLGPGTYDIHSPVVPTPEFIRGKMESFL 719
++ ++DADV SIE++RS++ETL Q Y +GPG YD+HSP +PT E++R + +
Sbjct: 644 SIKQLDADVISIEDSRSNNETLMQLTDADYPAQVGPGVYDVHSPSIPTTEYLRESLYKCI 703
Query: 720 ENMEVSQLTINPDCGLKTRGWPETIEALRVMVEVTKEMRLE 760
+ + V+Q+ +NPDCGLKTR W E I A R MV+ +R E
Sbjct: 704 QYLPVTQIWVNPDCGLKTRRWEEAIPATRNMVQAAISLRQE 744
Lambda K H
0.318 0.134 0.399
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: 1450
Number of extensions: 62
Number of successful extensions: 12
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: 765
Length of database: 744
Length adjustment: 40
Effective length of query: 725
Effective length of database: 704
Effective search space: 510400
Effective search space used: 510400
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: 55 (25.8 bits)
Align candidate WP_011610649.1 TERY_RS04005 (5-methyltetrahydropteroyltriglutamate--homocysteine 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.19907.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2e-287 942.1 0.0 2.2e-287 941.9 0.0 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011610649.1 TERY_RS04005 5-methyltetrahydrop
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011610649.1 TERY_RS04005 5-methyltetrahydropteroyltriglutamate--homocysteine methyltran
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 941.9 0.0 2.2e-287 2.2e-287 1 754 [] 8 744 .] 8 744 .] 0.97
Alignments for each domain:
== domain 1 score: 941.9 bits; conditional E-value: 2.2e-287
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lg+Prig++Re+kkale++w++kis++ellk ++++++ +++q++ag++ i ++d +lYD++Ld +
lcl|NCBI__GCF_000014265.1:WP_011610649.1 8 LGYPRIGKNREVKKALESFWQQKISADELLKIVREIEEASWQTQTKAGIERIGIGDATLYDQILDWSFR 76
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtekkdvaalemtkwfntnYhYlvPelskeeefklsknkllee 138
+g+ip+rf++ ++l++yFa+aRG+ +++ alemtkwf+tnYhYlvPe++++ + k + + le
lcl|NCBI__GCF_000014265.1:WP_011610649.1 77 FGIIPKRFQQF----QNLECYFAMARGK--DGILALEMTKWFDTNYHYLVPEITPDITPKADFSDFLET 139
**********8....4589********9..56************************************* PP
TIGR01371 139 ykeakelg.vetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqidePvl 206
+k+ak+ ++ P+++ pitf+ L++ + + e ++l +llp+Y+++l+kl++ g++++q+ eP+l
lcl|NCBI__GCF_000014265.1:WP_011610649.1 140 VKRAKKIIgKSAVPIIISPITFIRLSRLE---SVEFDNILAQLLPLYSDLLTKLKKLGISEIQLHEPAL 205
***998654999**************988...47899******************************** PP
TIGR01371 207 vldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelelakak 275
v+ s++ +++++ ay+el++ l++ l tYfd++ e++ +++lpv+++ lDl ++++ + +++++
lcl|NCBI__GCF_000014265.1:WP_011610649.1 206 VFGDSSNLKKQFEMAYAELAK--VGLNIHLVTYFDDLGETYPWVMKLPVTSISLDLTRGQNLELIKSYG 272
********************8..699**********************************9999***** PP
TIGR01371 276 feedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkell 344
f++dk+L aGv+d rniw+ +++++ll++l+ + ++ v++s+sl vp+d+++e kl ++l+++l
lcl|NCBI__GCF_000014265.1:WP_011610649.1 273 FPADKTLGAGVVDARNIWRIRTQEVTSLLEELKGII-PNISVQPSASLQFVPYDVRREVKLPEALRNVL 340
**********************************99.88****************************** PP
TIGR01371 345 afakekleelkvlkealegeaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeR 413
+fa++klee +l++al+g +++++++e+ + +++ k + a+ekvk++++alke+++rr+ s+ eR
lcl|NCBI__GCF_000014265.1:WP_011610649.1 341 SFAEQKLEETVLLSKALTG-KSNKSEIENIEIYWQEFYKFSP-ANEKVKSQIKALKETDFRRSMSYLER 407
******************9.4455566666556666666554.6899********************** PP
TIGR01371 414 aeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelglDvLvh 482
++q ++lP++PtttiGsfPqtk+vRk Ra+++kge++++eY + i ++i+ +i lqe +g+DvLvh
lcl|NCBI__GCF_000014265.1:WP_011610649.1 408 LDNQ---IKLPAFPTTTIGSFPQTKQVRKLRARYKKGELTQAEYLAQIDANIAYCIGLQEGMGMDVLVH 473
*987...78************************************************************ PP
TIGR01371 483 GefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsltskpvkGm 551
GefeR DmveyFge+l+G++ft++gWvqsYGsR+v+Ppii+gd+ rp++mt++e++ aqslt+kpvkGm
lcl|NCBI__GCF_000014265.1:WP_011610649.1 474 GEFERSDMVEYFGEQLDGYTFTTHGWVQSYGSRYVRPPIIFGDIYRPHAMTIREFEVAQSLTEKPVKGM 542
********************************************************************* PP
TIGR01371 552 LtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdkeeYldw 620
LtGPvt+lnWs++R D++r+e+a q+ala+r+e+kdLe+ag++ iq+Depa+ReglPl+++ ++eYl+w
lcl|NCBI__GCF_000014265.1:WP_011610649.1 543 LTGPVTMLNWSYPRTDISRQEQAFQLALAIREELKDLEKAGAAFIQVDEPAMREGLPLKQQRWHEYLNW 611
********************************************************************* PP
TIGR01371 621 aveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikkyekeiGl 689
av+aFrl+++ +++etq+hthmCYsef +i+e+i++ldaDvisie srs+ e l +l + +y++++G+
lcl|NCBI__GCF_000014265.1:WP_011610649.1 612 AVDAFRLSTAIARPETQVHTHMCYSEFGDIMESIKQLDADVISIEDSRSNNETLMQLTD-ADYPAQVGP 679
***********************************************************.77******* PP
TIGR01371 690 GvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelRek 754
GvyD+hsp +P++e l+e+l k +++lp ++WvnPDCGLktR+wee ++a +n+v+aa +lR++
lcl|NCBI__GCF_000014265.1:WP_011610649.1 680 GVYDVHSPSIPTTEYLRESLYKCIQYLPVTQIWVNPDCGLKTRRWEEAIPATRNMVQAAISLRQE 744
***********************************************************999985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (744 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 8.49
//
[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