Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_015820569.1 TERTU_RS20795 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000023025.1:WP_015820569.1
Length = 763
Score = 810 bits (2091), Expect = 0.0
Identities = 427/761 (56%), Positives = 526/761 (69%), Gaps = 21/761 (2%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LG+PR+G RELK E YW G++ ++L V ELR +HW Q+ D +PVGDF+
Sbjct: 5 HNLGYPRIGAARELKFVLEKYWRGDAHEQQLQGVASELRQQHWTHQQAC--DWVPVGDFS 62
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEPAA---------AAEMT 116
YD VL S++LGN+PAR + + ++ T F + RG G+ AA AAEMT
Sbjct: 63 LYDQVLDASVMLGNLPARFAHLPPT-ELATYFAVARG--VQGDEAASACGHHGGDAAEMT 119
Query: 117 KWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGE 176
KWF+TNYHY+VPE QF L +LL ++ EA LG + KPV+LGP+T+LWL K K +
Sbjct: 120 KWFDTNYHYLVPEVSADTQFSLNSERLLTQLAEAHRLGVRAKPVILGPLTYLWLAKAK-D 178
Query: 177 QFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQ- 235
D L+LL+ +LP YQ +L++LA G +WVQIDEP LV EL W A+ AY LQ +
Sbjct: 179 GSDPLALLDRLLPAYQTLLSQLADAGADWVQIDEPILVTELDHNWQHAFSRAYHGLQQRG 238
Query: 236 VKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRN 295
++LLL TYF + NL LPV G+H+D V G+DDV L L +LS G+++GRN
Sbjct: 239 IRLLLATYFGPLRDNLQLACQLPVAGIHLDAVRGRDDVPRLADWLGDHKVLSLGVVDGRN 298
Query: 296 VWRADLTEKYAQIKDIVGK--RDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKC 353
+WR DL + I K + LW+A SCSLLH P+D VET +D E++ W AFA QK
Sbjct: 299 IWRTDLNATLDWLAPIAEKFSQRLWLAPSCSLLHVPVDADVETDMDREIQGWLAFARQKL 358
Query: 354 HELALLRDALNSG-DTAA--LAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVY 410
EL LLR ALN G D+ A LA ++ I+ARR S RV AV+K A + QRA+ Y
Sbjct: 359 AELTLLRHALNHGRDSVAGQLAANASAIRARRESRRVTVAAVQKHFAQVDGSWGQRASAY 418
Query: 411 EVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIV 470
R+E Q A LP +PTTTIGSFPQT +IR +R +K G L NYR +A I +A+
Sbjct: 419 PQRSEKQAAILALPPFPTTTIGSFPQTADIRKVRKQYKSGALSEQNYRAAMAAAIAEAVS 478
Query: 471 EQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPA 530
QE+LGLDVLVHGEAERNDMVEYFGE L+GFVF++ GWVQSYGSRCVKPPI+ GDI RP
Sbjct: 479 IQEQLGLDVLVHGEAERNDMVEYFGEQLEGFVFSRCGWVQSYGSRCVKPPIIYGDIQRPY 538
Query: 531 PITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEA 590
P+TV+W KYAQSLT KP+KGMLTGPVT+L WSF R+D R +Q+ALA+R EV DLE
Sbjct: 539 PMTVDWIKYAQSLTSKPMKGMLTGPVTMLNWSFVRDDQPRSLTCQQLALAIRAEVQDLER 598
Query: 591 AGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDI 650
AGIGIIQIDE ALREGLPLRRS+W YL W VEAFR+ A D+TQIHTHMCY EFNDI
Sbjct: 599 AGIGIIQIDEAALREGLPLRRSEWQGYLNWAVEAFRVAANGVADETQIHTHMCYSEFNDI 658
Query: 651 MDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKK 710
+ +IA +DADVITIETSRS MELL+ F +F YPN+IGPGVYDIHSP +PS E + AL+ +
Sbjct: 659 IGAIAHMDADVITIETSRSHMELLDVFRDFHYPNQIGPGVYDIHSPAIPSAEQMVALITR 718
Query: 711 AAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
AA+ IPAERLWVNPDCGLKTR W E AL +MV AAQ LR
Sbjct: 719 AAQTIPAERLWVNPDCGLKTRRWEEVLPALRHMVNAAQTLR 759
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: 1719
Number of extensions: 87
Number of successful extensions: 10
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: 763
Length adjustment: 40
Effective length of query: 713
Effective length of database: 723
Effective search space: 515499
Effective search space used: 515499
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_015820569.1 TERTU_RS20795 (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.16398.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 1086.5 0.0 0 1086.3 0.0 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015820569.1 TERTU_RS20795 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015820569.1 TERTU_RS20795 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1086.3 0.0 0 0 1 754 [] 7 761 .. 7 761 .. 0.98
Alignments for each domain:
== domain 1 score: 1086.3 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lg+Prig+ Relk+ lekyw+g+ ++++l+ va++lr++++++q++ d +pv+dfslYD+vLd++v+
lcl|NCBI__GCF_000023025.1:WP_015820569.1 7 LGYPRIGAARELKFVLEKYWRGDAHEQQLQGVASELRQQHWTHQQA--CDWVPVGDFSLYDQVLDASVM 73
79****************************************9995..6******************** PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek.........kdvaalemtkwfntnYhYlvPelskeeefk 129
lg++p+rf +l ++l+tyFa+aRG + ++ a emtkwf+tnYhYlvPe+s++++f+
lcl|NCBI__GCF_000023025.1:WP_015820569.1 74 LGNLPARFAHLP--PTELATYFAVARGVQGdeaasacghHGGDAAEMTKWFDTNYHYLVPEVSADTQFS 140
**********94..456***********999999999997778************************** PP
TIGR01371 130 lsknklleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvew 198
l++++ll ++ ea++lgv +kPv+lGp+t+l+Lakak+ +++l+ll++llp+Y+ +l++la+ag++w
lcl|NCBI__GCF_000023025.1:WP_015820569.1 141 LNSERLLTQLAEAHRLGVRAKPVILGPLTYLWLAKAKD--GSDPLALLDRLLPAYQTLLSQLADAGADW 207
*************************************8..569************************** PP
TIGR01371 199 vqidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveake 267
vqideP+lv++l++++++a+ +ay+ l++ + +lll+tYf+ ++++l+ + +lpv++++lD v++++
lcl|NCBI__GCF_000023025.1:WP_015820569.1 208 VQIDEPILVTELDHNWQHAFSRAYHGLQQ--RGIRLLLATYFGPLRDNLQLACQLPVAGIHLDAVRGRD 274
***************************97..699*********************************** PP
TIGR01371 268 elelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekl 336
+ + + ++kvL++Gv+dGrniw++dl+++l+ l+ +++k +++l++++scsllhvpvd + e+++
lcl|NCBI__GCF_000023025.1:WP_015820569.1 275 DVPRLADWLGDHKVLSLGVVDGRNIWRTDLNATLDWLAPIAEKFSQRLWLAPSCSLLHVPVDADVETDM 343
*88888889999********************************************************* PP
TIGR01371 337 dkelkellafakekleelkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekka 404
d+e++ +lafa++kl+el++l++al++ +++va +l+a+a+ai+ar++s+rv+ ++v+++ ++++ +
lcl|NCBI__GCF_000023025.1:WP_015820569.1 344 DREIQGWLAFARQKLAELTLLRHALNHgRDSVAGQLAANASAIRARRESRRVTVAAVQKHFAQVDGSWG 412
**************************99***************************************** PP
TIGR01371 405 rressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqe 473
+r+s + +R+e+q++ l lP +PtttiGsfPqt+++Rk+R++++ g +se++Y +++ + i++++++qe
lcl|NCBI__GCF_000023025.1:WP_015820569.1 413 QRASAYPQRSEKQAAILALPPFPTTTIGSFPQTADIRKVRKQYKSGALSEQNYRAAMAAAIAEAVSIQE 481
********************************************************************* PP
TIGR01371 474 elglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqs 542
+lglDvLvhGe+eRnDmveyFge+l+Gf+f + gWvqsYGsRcvkPpiiygd++rp pmtv+++kyaqs
lcl|NCBI__GCF_000023025.1:WP_015820569.1 482 QLGLDVLVHGEAERNDMVEYFGEQLEGFVFSRCGWVQSYGSRCVKPPIIYGDIQRPYPMTVDWIKYAQS 550
********************************************************************* PP
TIGR01371 543 ltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrk 611
ltskp+kGmLtGPvt+lnWsfvR+D+pr+ +++q+ala+r ev+dLe agi iiqiDe+alReglPlr+
lcl|NCBI__GCF_000023025.1:WP_015820569.1 551 LTSKPMKGMLTGPVTMLNWSFVRDDQPRSLTCQQLALAIRAEVQDLERAGIGIIQIDEAALREGLPLRR 619
********************************************************************* PP
TIGR01371 612 sdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkei 680
s+++ Yl+waveaFr+aa+gv+detqihthmCYsefn+ii aia++daDvi+ie+srs+melld +++
lcl|NCBI__GCF_000023025.1:WP_015820569.1 620 SEWQGYLNWAVEAFRVAANGVADETQIHTHMCYSEFNDIIGAIAHMDADVITIETSRSHMELLDVFRD- 687
********************************************************************. PP
TIGR01371 681 kkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaak 749
++y+++iG+GvyDihsp++Ps+e++ +l+++a +++p+erlWvnPDCGLktR+weev +al+++v+aa+
lcl|NCBI__GCF_000023025.1:WP_015820569.1 688 FHYPNQIGPGVYDIHSPAIPSAEQMVALITRAAQTIPAERLWVNPDCGLKTRRWEEVLPALRHMVNAAQ 756
66******************************************************************* PP
TIGR01371 750 elRek 754
+lRek
lcl|NCBI__GCF_000023025.1:WP_015820569.1 757 TLREK 761
***96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (763 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: 8.38
//
[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