Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_086508046.1 BZY95_RS00525 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_002151265.1:WP_086508046.1
Length = 765
Score = 910 bits (2351), Expect = 0.0
Identities = 459/761 (60%), Positives = 559/761 (73%), Gaps = 13/761 (1%)
Query: 4 LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
L H LG+PR+G RELK+A E+YW G R+ L A RELRARHW Q+ AG+DL+ VGD
Sbjct: 3 LAHVLGYPRIGADRELKRAVEAYWRGELDRDALEASARELRARHWQAQRDAGLDLVTVGD 62
Query: 64 FAWYDHVLTTSLLLGNVPARHQNKD----GSVDIDTLFRIGRGRAPTGEPAAAAEMTKWF 119
FA+YD VL S ++G VP R ++ G VD+DT FR+ RGRAP+G PAAA EMTK+F
Sbjct: 63 FAFYDQVLNVSAMVGAVPTRFAAEEEVARGEVDLDTQFRMARGRAPSGAPAAACEMTKYF 122
Query: 120 NTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQFD 179
+TNYHY+VPE GQQF+L T+L DEV EA GH VK L GP+TWLWLGK + FD
Sbjct: 123 DTNYHYLVPELHAGQQFRLASTRLFDEVAEARGAGHPVKVALTGPLTWLWLGKGREAGFD 182
Query: 180 RLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQGQ-VKL 238
RLSLL +LPVY ++LA LA++G+EWVQ+DEPALV +LP W +AY+ AY +L+ VKL
Sbjct: 183 RLSLLPALLPVYGEILARLAEQGVEWVQLDEPALVQDLPLEWRNAYEFAYSSLRAAPVKL 242
Query: 239 LLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWR 298
LL TYF G+ NL +LPV GLH+D V + + + L +LS G I+GRNVWR
Sbjct: 243 LLATYFGGLGDNLRLAASLPVDGLHIDTVRAPEQLTAVLDNLSGYKVLSVGAIDGRNVWR 302
Query: 299 ADLT---EKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHE 355
ADL E+ A + +G+R LW+A SCSLLH P+DL+ ET LD E+KSW AFA QK E
Sbjct: 303 ADLAVLHERLANTRMRLGER-LWLAPSCSLLHVPVDLAAETTLDEELKSWLAFARQKLDE 361
Query: 356 LALLRDAL-NSG---DTAALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYE 411
L L N G D A +A +A + RR S R+H P V +RLA + + R N Y
Sbjct: 362 TVTLARLLGNRGTDEDRARVAAATAALDTRRASPRLHRPEVAERLAGVGDAERSRDNPYP 421
Query: 412 VRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVE 471
VRA AQR LP +PTTTIGSFPQT IR R FK G L + Y + + I A+
Sbjct: 422 VRARAQRRALDLPLFPTTTIGSFPQTAGIRAARRAFKSGELGHDAYEAAMRDEIADAVRR 481
Query: 472 QERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAP 531
QE G+D+LVHGEAERNDMVEYFGE LDG+ FT+NGWVQSYGSRCVKPP+++GD++RPAP
Sbjct: 482 QEAYGIDMLVHGEAERNDMVEYFGEQLDGYAFTRNGWVQSYGSRCVKPPVIVGDVARPAP 541
Query: 532 ITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAA 591
+TV W++YAQSLT++P+KGMLTGPVT+L WSF R+D RE +QIALALRDEVADLEAA
Sbjct: 542 MTVAWSRYAQSLTERPMKGMLTGPVTMLQWSFVRDDQPREVTCRQIALALRDEVADLEAA 601
Query: 592 GIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIM 651
GI IQIDEPALREGLPLR+S+W +YL W VE FR+ A+VA+D TQIHTHMCY EFNDI+
Sbjct: 602 GIPAIQIDEPALREGLPLRQSEWQSYLDWAVECFRLTASVARDATQIHTHMCYSEFNDII 661
Query: 652 DSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKA 711
+IAALDADVITIETSRS+MELL++F++F YPNEIGPGVYDIHSPNVP V W+ L++KA
Sbjct: 662 GAIAALDADVITIETSRSNMELLDAFQDFAYPNEIGPGVYDIHSPNVPEVAWMVQLMEKA 721
Query: 712 AKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLRR 752
A+RIP ERLWVNPDCGLKTR W E ALANMV+AA+ LRR
Sbjct: 722 AERIPVERLWVNPDCGLKTRSWAEVEPALANMVEAARELRR 762
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: 1781
Number of extensions: 78
Number of successful extensions: 9
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: 765
Length adjustment: 40
Effective length of query: 713
Effective length of database: 725
Effective search space: 516925
Effective search space used: 516925
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_086508046.1 BZY95_RS00525 (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.1631.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 1056.1 0.0 0 1055.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508046.1 BZY95_RS00525 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508046.1 BZY95_RS00525 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1055.9 0.0 0 0 1 753 [. 7 762 .. 7 763 .. 0.98
Alignments for each domain:
== domain 1 score: 1055.9 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lg+Prig+ Relk+a+e+yw+g++++++l+++a++lr++++++q++ag+d+++v+df++YD+vL+++++
lcl|NCBI__GCF_002151265.1:WP_086508046.1 7 LGYPRIGADRELKRAVEAYWRGELDRDALEASARELRARHWQAQRDAGLDLVTVGDFAFYDQVLNVSAM 75
79******************************************************************* PP
TIGR01371 70 lgaiperfk...eladdesdldtyFaiaRGtek..kdvaalemtkwfntnYhYlvPelskeeefklskn 133
+ga+p+rf e+a +e+dldt F++aRG + +aa+emtk+f+tnYhYlvPel++ ++f+l+++
lcl|NCBI__GCF_002151265.1:WP_086508046.1 76 VGAVPTRFAaeeEVARGEVDLDTQFRMARGRAPsgAPAAACEMTKYFDTNYHYLVPELHAGQQFRLAST 144
********722245678899**********98844557899**************************** PP
TIGR01371 134 klleeykeakelgvetkPvllGpitflkLakakeeeekellellekllpvYkevlkklaeagvewvqid 202
+l++e+ ea+ +g+ +k l Gp+t+l+L+k e +++l+ll++llpvY e+l +lae+gvewvq+d
lcl|NCBI__GCF_002151265.1:WP_086508046.1 145 RLFDEVAEARGAGHPVKVALTGPLTWLWLGKGRE-AGFDRLSLLPALLPVYGEILARLAEQGVEWVQLD 212
********************************96.88******************************** PP
TIGR01371 203 ePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeelel 271
eP+lv dl+ e+++a++ ay++l+ + +klll+tYf+ + ++l+ ++slpv++l++D v+a+e+l++
lcl|NCBI__GCF_002151265.1:WP_086508046.1 213 EPALVQDLPLEWRNAYEFAYSSLRA--APVKLLLATYFGGLGDNLRLAASLPVDGLHIDTVRAPEQLTA 279
************************7..699*************************************** PP
TIGR01371 272 akakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkel 340
+ +++ kvL++G idGrn+w+adl+ +++l++ + g++l++++scsllhvpvdl +e++ld+el
lcl|NCBI__GCF_002151265.1:WP_086508046.1 280 VLDNLSGYKVLSVGAIDGRNVWRADLAVLHERLANTRMRLGERLWLAPSCSLLHVPVDLAAETTLDEEL 348
********************************************************************* PP
TIGR01371 341 kellafakekleelkvlkealeg..eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarre 407
k++lafa++kl+e +l+++l + ++++ ++++a++aa+ +r+ s+r + +v+erl+ + +++ r
lcl|NCBI__GCF_002151265.1:WP_086508046.1 349 KSWLAFARQKLDETVTLARLLGNrgTDEDRARVAAATAALDTRRASPRLHRPEVAERLAGVGDAERSRD 417
*********************776689999999999********************************* PP
TIGR01371 408 ssfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelg 476
+++ Ra+aq++ l+lPl+PtttiGsfPqt+ +R aR++f+ ge+ +++Ye+++++ei+++++ qe+ g
lcl|NCBI__GCF_002151265.1:WP_086508046.1 418 NPYPVRARAQRRALDLPLFPTTTIGSFPQTAGIRAARRAFKSGELGHDAYEAAMRDEIADAVRRQEAYG 486
********************************************************************* PP
TIGR01371 477 lDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqslts 545
+D+LvhGe+eRnDmveyFge+l+G+aft+ngWvqsYGsRcvkPp+i+gdv rp+pmtv++s+yaqslt+
lcl|NCBI__GCF_002151265.1:WP_086508046.1 487 IDMLVHGEAERNDMVEYFGEQLDGYAFTRNGWVQSYGSRCVKPPVIVGDVARPAPMTVAWSRYAQSLTE 555
********************************************************************* PP
TIGR01371 546 kpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrksdk 614
+p+kGmLtGPvt+l+WsfvR+D+pr+ +++qialalrdev+dLe+agi iqiDepalReglPlr+s++
lcl|NCBI__GCF_002151265.1:WP_086508046.1 556 RPMKGMLTGPVTMLQWSFVRDDQPREVTCRQIALALRDEVADLEAAGIPAIQIDEPALREGLPLRQSEW 624
********************************************************************* PP
TIGR01371 615 eeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeikky 683
++Yldwave Frl+as ++d+tqihthmCYsefn+ii aiaaldaDvi+ie+srs+mellda+++ ++y
lcl|NCBI__GCF_002151265.1:WP_086508046.1 625 QSYLDWAVECFRLTASVARDATQIHTHMCYSEFNDIIGAIAALDADVITIETSRSNMELLDAFQD-FAY 692
*****************************************************************.66* PP
TIGR01371 684 ekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaakelR 752
++eiG+GvyDihsp+vP + ++ +l+eka +++p erlWvnPDCGLktR+w ev++al n+veaa+elR
lcl|NCBI__GCF_002151265.1:WP_086508046.1 693 PNEIGPGVYDIHSPNVPEVAWMVQLMEKAAERIPVERLWVNPDCGLKTRSWAEVEPALANMVEAARELR 761
*******************************************************************99 PP
TIGR01371 753 e 753
lcl|NCBI__GCF_002151265.1:WP_086508046.1 762 R 762
6 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (765 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: 00:00:00.05
# Mc/sec: 10.57
//
[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