Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_013722046.1 ALIDE2_RS10440 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000204645.1:WP_013722046.1
Length = 786
Score = 801 bits (2069), Expect = 0.0
Identities = 423/773 (54%), Positives = 512/773 (66%), Gaps = 24/773 (3%)
Query: 3 ILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVG 62
+L HTLGFPR+G +RELK A E +W G L AVG ELR RHW Q+ AG+ + VG
Sbjct: 6 VLTHTLGFPRMGAQRELKFALERHWRGEIDAAALEAVGAELRTRHWQAQRDAGLAFVTVG 65
Query: 63 DFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRG-----------------RAP 105
DFA+YDHV LLG AR + ++ F + RG A
Sbjct: 66 DFAFYDHVANHIQLLGCESARFGFAPDTPELARYFAMARGVQAQAHGAPGCGAGCTHAAH 125
Query: 106 TGEPAAAAEMTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPV 165
G +A EMTKWF+TNYHY+VPE G F L +L EV +A ALGH+VK VL+GP+
Sbjct: 126 EGAGQSALEMTKWFDTNYHYLVPELHAGTAFSLASERLFGEVAQAQALGHRVKAVLVGPL 185
Query: 166 TWLWLGKVKGEQ-FDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDA 224
T+LWL K KG+ FDRL+LL+ +LPVY Q+LA L +G+EWVQIDEP L L+LP AW A
Sbjct: 186 TFLWLSKEKGDTPFDRLALLDRLLPVYAQILARLKAQGVEWVQIDEPILGLDLPAAWSQA 245
Query: 225 YKPAYDAL-QGQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSD 283
++PAY L + ++LL TYF + +L LPV GLHVD V ++ + LP
Sbjct: 246 FEPAYWQLGKAGPQVLLATYFSPLEDHLRLACQLPVAGLHVDAVRAPHELTGVADWLPGY 305
Query: 284 WLLSAGLINGRNVWRADLTEKYAQIKDIVGKRD--LWVASSCSLLHSPIDLSVETRLDAE 341
+LS G+++GRN+WR D A ++ + K LW+A SCSLLH P+ L+ E LDAE
Sbjct: 306 KVLSVGVVDGRNIWRTDPDAALALLRPVADKHQGPLWIAPSCSLLHVPVSLAGEDALDAE 365
Query: 342 VKSWFAFALQKCHELALLRDALN--SGD-TAALAEWSAPIQARRHSTRVHNPAVEKRLAA 398
++SW FA +K EL LL L+ +GD LA+ A +RR S RVH P V +RLA
Sbjct: 366 LRSWLTFATEKLGELGLLAALLDGRAGDGDPRLADARAAAASRRASARVHRPEVTRRLAG 425
Query: 399 ITAQDSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYR 458
+R + R QR R +LP PTTTIGSFPQT IR R ++G LD Y+
Sbjct: 426 APEGADRRRAPFPARQAVQRTRLRLPLLPTTTIGSFPQTPAIRAARAAHRRGALDDAEYQ 485
Query: 459 TGIAEHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVK 518
+ I A+ QE LGLDVLVHGEAERNDMVEYFGE LDGF FTQNGWVQSYGSRCVK
Sbjct: 486 ARMRAEIAHAVRTQEALGLDVLVHGEAERNDMVEYFGEQLDGFAFTQNGWVQSYGSRCVK 545
Query: 519 PPIVIGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIA 578
PP++ GD++RP P+TV+W YAQSLT +P+KGMLTGPVTIL WSF R+D R +QIA
Sbjct: 546 PPVLYGDVARPRPMTVDWTVYAQSLTPRPMKGMLTGPVTILQWSFVRDDQPRSRTCEQIA 605
Query: 579 LALRDEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQI 638
A+RDEVADLE AGIGI+QIDEPA+REGLPLRR+ W YL W AFRI A D TQI
Sbjct: 606 WAIRDEVADLERAGIGIVQIDEPAIREGLPLRRAHWKPYLDWATRAFRIAACGVGDATQI 665
Query: 639 HTHMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNV 698
HTHMCY EFNDI+ IAA+DADVITIETSRS MELL+ F F YPNEIGPGVYDIHSP V
Sbjct: 666 HTHMCYSEFNDILPGIAAMDADVITIETSRSGMELLQGFGTFKYPNEIGPGVYDIHSPRV 725
Query: 699 PSVEWIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
P V+ + LL++AA+ +P LWVNPDCGLKTR WPET AAL NMVQAA LR
Sbjct: 726 PGVDEMLRLLRRAAEVVPPGNLWVNPDCGLKTRAWPETEAALRNMVQAAGALR 778
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: 1718
Number of extensions: 86
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: 786
Length adjustment: 41
Effective length of query: 712
Effective length of database: 745
Effective search space: 530440
Effective search space used: 530440
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_013722046.1 ALIDE2_RS10440 (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.3381.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 1030.3 0.0 0 1030.1 0.0 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013722046.1 ALIDE2_RS10440 5-methyltetrahydr
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013722046.1 ALIDE2_RS10440 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyl
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1030.1 0.0 0 0 1 753 [. 11 779 .. 11 780 .. 0.99
Alignments for each domain:
== domain 1 score: 1030.1 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPr+g++Relk+ale++w+g+i++++l++v ++lr++++++q++ag+ +++v+df++YDhv + l
lcl|NCBI__GCF_000204645.1:WP_013722046.1 11 LGFPRMGAQRELKFALERHWRGEIDAAALEAVGAELRTRHWQAQRDAGLAFVTVGDFAFYDHVANHIQL 79
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek...................kdvaalemtkwfntnYhYlv 119
lg +rf d+ +l++yFa+aRG + + +alemtkwf+tnYhYlv
lcl|NCBI__GCF_000204645.1:WP_013722046.1 80 LGCESARFGFA-PDTPELARYFAMARGVQAqahgapgcgagcthaahegAGQSALEMTKWFDTNYHYLV 147
*********98.66679***********989****************99889***************** PP
TIGR01371 120 PelskeeefklsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevl 188
Pel++ ++f+l++++l+ e+ +a++lg+ +k vl+Gp+tfl+L+k+k ++ +++l+ll++llpvY ++l
lcl|NCBI__GCF_000204645.1:WP_013722046.1 148 PELHAGTAFSLASERLFGEVAQAQALGHRVKAVLVGPLTFLWLSKEKGDTPFDRLALLDRLLPVYAQIL 216
********************************************************************* PP
TIGR01371 189 kklaeagvewvqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvea 257
+l+++gvewvqideP+l ldl++++ +a++ ay +l + + ++ll+tYf +e++l+ + +lpv++
lcl|NCBI__GCF_000204645.1:WP_013722046.1 217 ARLKAQGVEWVQIDEPILGLDLPAAWSQAFEPAYWQLGK--AGPQVLLATYFSPLEDHLRLACQLPVAG 283
**************************************8..699************************* PP
TIGR01371 258 lglDlveakeelelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhv 326
l++D v+a++el+ ++ ++ kvL++Gv+dGrniw++d ++l+ll+ +++k++ l++++scsllhv
lcl|NCBI__GCF_000204645.1:WP_013722046.1 284 LHVDAVRAPHELTGVADWLPGYKVLSVGVVDGRNIWRTDPDAALALLRPVADKHQGPLWIAPSCSLLHV 352
***********9999999*************************************99************ PP
TIGR01371 327 pvdleleekldkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvke 394
pv+l e++ld+el+++l+fa+ekl el +l+ +l+g + +l++++aa a+r+ s+rv+ +v++
lcl|NCBI__GCF_000204645.1:WP_013722046.1 353 PVSLAGEDALDAELRSWLTFATEKLGELGLLAALLDGrAGDGDPRLADARAAAASRRASARVHRPEVTR 421
*************************************767777889999999***************** PP
TIGR01371 395 rlealkekkarressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfike 463
rl+ e rr+++f +R++ q+ +l+lPllPtttiGsfPqt +R aRa++r+g ++++eY++ +++
lcl|NCBI__GCF_000204645.1:WP_013722046.1 422 RLAGAPEGADRRRAPFPARQAVQRTRLRLPLLPTTTIGSFPQTPAIRAARAAHRRGALDDAEYQARMRA 490
********************************************************************* PP
TIGR01371 464 eikkviklqeelglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpm 532
ei++++++qe+lglDvLvhGe+eRnDmveyFge+l+GfaftqngWvqsYGsRcvkPp++ygdv rp+pm
lcl|NCBI__GCF_000204645.1:WP_013722046.1 491 EIAHAVRTQEALGLDVLVHGEAERNDMVEYFGEQLDGFAFTQNGWVQSYGSRCVKPPVLYGDVARPRPM 559
********************************************************************* PP
TIGR01371 533 tvkeskyaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDep 601
tv++++yaqslt +p+kGmLtGPvtil+WsfvR+D+pr++++eqia a+rdev+dLe agi i+qiDep
lcl|NCBI__GCF_000204645.1:WP_013722046.1 560 TVDWTVYAQSLTPRPMKGMLTGPVTILQWSFVRDDQPRSRTCEQIAWAIRDEVADLERAGIGIVQIDEP 628
********************************************************************* PP
TIGR01371 602 alReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsd 670
a+ReglPlr+++++ Yldwa +aFr+aa+gv d+tqihthmCYsefn+i+ iaa+daDvi+ie+srs
lcl|NCBI__GCF_000204645.1:WP_013722046.1 629 AIREGLPLRRAHWKPYLDWATRAFRIAACGVGDATQIHTHMCYSEFNDILPGIAAMDADVITIETSRSG 697
********************************************************************* PP
TIGR01371 671 melldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevka 739
mell+ + +ky++eiG+GvyDihsprvP ++e+ +ll++a +++p +lWvnPDCGLktR+w+e++a
lcl|NCBI__GCF_000204645.1:WP_013722046.1 698 MELLQGFGT-FKYPNEIGPGVYDIHSPRVPGVDEMLRLLRRAAEVVPPGNLWVNPDCGLKTRAWPETEA 765
********9.77********************************************************* PP
TIGR01371 740 alknlveaakelRe 753
al+n+v+aa +lR+
lcl|NCBI__GCF_000204645.1:WP_013722046.1 766 ALRNMVQAAGALRA 779
**********9997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (786 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 11.96
//
[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