Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_090447968.1 BLS63_RS22140 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_900100495.1:WP_090447968.1
Length = 768
Score = 923 bits (2386), Expect = 0.0
Identities = 469/762 (61%), Positives = 563/762 (73%), Gaps = 14/762 (1%)
Query: 4 LNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGD 63
L+H+LGFPR+G RELKKA E++W G L AVGRELRA HW QK AG+DLLPVGD
Sbjct: 3 LSHSLGFPRIGRDRELKKALEAHWKGELDEAGLRAVGRELRAAHWQLQKDAGLDLLPVGD 62
Query: 64 FAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAP--TGEPAAAAEMTKWFNT 121
FAWYD VL+ SL G +PAR + DG +DTLF + RG G A A E+TKWF+T
Sbjct: 63 FAWYDQVLSHSLAFGVIPARFRPADGKPSLDTLFAMARGAGQGCCGGGAHAQELTKWFDT 122
Query: 122 NYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQ---- 177
NYHY+VPEF Q+F+L+W QL +EV EA ALGHKVKPVL+GP+++LWLGKVKG
Sbjct: 123 NYHYLVPEFSVDQRFQLSWEQLFEEVAEAHALGHKVKPVLIGPLSYLWLGKVKGAAAEVG 182
Query: 178 -FDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQ 235
FD+L LL +LPVY ++L LA +G+EWVQIDEP L L+LPQ W +A++ AY LQ
Sbjct: 183 GFDKLELLERLLPVYGEILGRLAAQGVEWVQIDEPILGLDLPQDWKNAFERAYHLLQHAP 242
Query: 236 VKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRN 295
+K L+ YF G+ NL +LPV GLHVDLV + + L RLPS +LS G++NGRN
Sbjct: 243 LKKLVACYFSGLEDNLGLAVSLPVDGLHVDLVRAPEQLPLLLDRLPSYKVLSLGVVNGRN 302
Query: 296 VWRADLTEKYAQIKDIVGK--RDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKC 353
VWR DL + Q+ + +LWVA SCSLLHSP+DL+ E +LDAE+K W AFA+QKC
Sbjct: 303 VWRCDLDQALDQLHQAQERFAGNLWVAGSCSLLHSPVDLAREDQLDAELKGWLAFAVQKC 362
Query: 354 HELALLRDALNSGDTA----ALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANV 409
E+A+L ALN A ALA A +R STR+H PAV+ RLAAIT DSQRA
Sbjct: 363 AEIAVLARALNQPQAAEVQTALAASRAVQASRVGSTRIHKPAVQARLAAITPADSQRAAP 422
Query: 410 YEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAI 469
+ R E QRAR +LPA PTTTIGSFPQT IR R FK+G L A +Y + I+ A+
Sbjct: 423 FAARIEQQRARLQLPALPTTTIGSFPQTAAIRLARQAFKQGKLSAADYTEAMHSEIRHAV 482
Query: 470 VEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRP 529
QE LGLDVLVHGEAERNDMVEYF E LDG+ F++ GWVQSYGSRCVKP +++GD+SRP
Sbjct: 483 EVQENLGLDVLVHGEAERNDMVEYFAEQLDGYAFSRFGWVQSYGSRCVKPAVIVGDLSRP 542
Query: 530 APITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLE 589
P+TVEW +YAQ LT K +KGMLTGPVT+L WSFPRED+SRE A+Q+ALA+RDEV DLE
Sbjct: 543 QPMTVEWIRYAQGLTAKVMKGMLTGPVTMLMWSFPREDISREQQARQLALAIRDEVQDLE 602
Query: 590 AAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFND 649
AAGI I+QIDE A REGLPLRR+ W AYL W EAFR+ A+ +D+TQIHTHMCY EFND
Sbjct: 603 AAGIRIVQIDEAAFREGLPLRRAQWAAYLDWATEAFRLCASGVRDETQIHTHMCYSEFND 662
Query: 650 IMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLK 709
++++IAA+DADVITIETSRSDMELL++FE FDYPNEIGPGVYDIHSP VP + LL+
Sbjct: 663 VIEAIAAMDADVITIETSRSDMELLKAFEAFDYPNEIGPGVYDIHSPRVPDSVEMARLLR 722
Query: 710 KAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
KAA+RIPAERLWVNPDCGLKTR W ET AAL NMV AA+ LR
Sbjct: 723 KAARRIPAERLWVNPDCGLKTRAWAETEAALVNMVAAARQLR 764
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: 1707
Number of extensions: 71
Number of successful extensions: 7
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: 768
Length adjustment: 40
Effective length of query: 713
Effective length of database: 728
Effective search space: 519064
Effective search space used: 519064
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_090447968.1 BLS63_RS22140 (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.435.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 1080.5 0.0 0 1080.4 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090447968.1 BLS63_RS22140 5-methyltetrahydro
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447968.1 BLS63_RS22140 5-methyltetrahydropteroyltriglutamate--homocysteine S-methylt
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1080.4 0.0 0 0 1 753 [. 7 765 .. 7 766 .. 0.97
Alignments for each domain:
== domain 1 score: 1080.4 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig+ Relkkale++wkg+++++ l +v ++lr+ +++ qk+ag+d++pv+df++YD+vL ++
lcl|NCBI__GCF_900100495.1:WP_090447968.1 7 LGFPRIGRDRELKKALEAHWKGELDEAGLRAVGRELRAAHWQLQKDAGLDLLPVGDFAWYDQVLSHSLA 75
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek....kdvaalemtkwfntnYhYlvPelskeeefklsknk 134
+g+ip+rf+ d++ +ldt+Fa+aRG + +++a+e+tkwf+tnYhYlvPe+s +++f+ls+++
lcl|NCBI__GCF_900100495.1:WP_090447968.1 76 FGVIPARFRPA-DGKPSLDTLFAMARGAGQgccgGGAHAQELTKWFDTNYHYLVPEFSVDQRFQLSWEQ 143
**********8.67779**********9889999899******************************** PP
TIGR01371 135 lleeykeakelgvetkPvllGpitflkLakakee....eekellellekllpvYkevlkklaeagvewv 199
l+ee+ ea++lg+++kPvl+Gp+++l+L+k k + +++lelle+llpvY e+l +la++gvewv
lcl|NCBI__GCF_900100495.1:WP_090447968.1 144 LFEEVAEAHALGHKVKPVLIGPLSYLWLGKVKGAaaevGGFDKLELLERLLPVYGEILGRLAAQGVEWV 212
******************************987655556799*************************** PP
TIGR01371 200 qidePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakee 268
qideP+l ldl++++++a+++ay+ l++a lk l++ Yf +e++l +vslpv++l++Dlv+a+e+
lcl|NCBI__GCF_900100495.1:WP_090447968.1 213 QIDEPILGLDLPQDWKNAFERAYHLLQHA--PLKKLVACYFSGLEDNLGLAVSLPVDGLHVDLVRAPEQ 279
**************************984..677789******************************** PP
TIGR01371 269 lelakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekld 337
l l ++++ kvL++Gv++Grn+w+ dl ++l++l++ +++ + +l+v+ scsllh+pvdl +e++ld
lcl|NCBI__GCF_900100495.1:WP_090447968.1 280 LPLLLDRLPSYKVLSLGVVNGRNVWRCDLDQALDQLHQAQERFAGNLWVAGSCSLLHSPVDLAREDQLD 348
********************************************99*********************** PP
TIGR01371 338 kelkellafakekleelkvlkealeg..eaavaealeaeaaaiaarkkskrvadekvkerlealkekka 404
+elk +lafa++k++e++vl++al++ a+v++al+a++a a+r s+r+++ +v++rl+a++ +++
lcl|NCBI__GCF_900100495.1:WP_090447968.1 349 AELKGWLAFAVQKCAEIAVLARALNQpqAAEVQTALAASRAVQASRVGSTRIHKPAVQARLAAITPADS 417
**************************934455566666666667788899******************* PP
TIGR01371 405 rressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqe 473
+r+++f++R e+q+++l+lP+lPtttiGsfPqt+ +R aR++f++g++s+++Y++++++ei++++++qe
lcl|NCBI__GCF_900100495.1:WP_090447968.1 418 QRAAPFAARIEQQRARLQLPALPTTTIGSFPQTAAIRLARQAFKQGKLSAADYTEAMHSEIRHAVEVQE 486
********************************************************************* PP
TIGR01371 474 elglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqs 542
+lglDvLvhGe+eRnDmveyF+e+l+G+af ++gWvqsYGsRcvkP++i+gd+srp+pmtv++++yaq+
lcl|NCBI__GCF_900100495.1:WP_090447968.1 487 NLGLDVLVHGEAERNDMVEYFAEQLDGYAFSRFGWVQSYGSRCVKPAVIVGDLSRPQPMTVEWIRYAQG 555
********************************************************************* PP
TIGR01371 543 ltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrk 611
lt k +kGmLtGPvt+l Wsf+ReD++r+++a+q+ala+rdev+dLe+agi+i+qiDe+a+ReglPlr+
lcl|NCBI__GCF_900100495.1:WP_090447968.1 556 LTAKVMKGMLTGPVTMLMWSFPREDISREQQARQLALAIRDEVQDLEAAGIRIVQIDEAAFREGLPLRR 624
********************************************************************* PP
TIGR01371 612 sdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkei 680
+++++Yldwa eaFrl asgv+detqihthmCYsefn++ieaiaa+daDvi+ie+srsdmell+a+++
lcl|NCBI__GCF_900100495.1:WP_090447968.1 625 AQWAAYLDWATEAFRLCASGVRDETQIHTHMCYSEFNDVIEAIAAMDADVITIETSRSDMELLKAFEA- 692
********************************************************************. PP
TIGR01371 681 kkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaak 749
++y++eiG+GvyDihsprvP + e+a+ll+ka +++p+erlWvnPDCGLktR+w e++aal n+v+aa+
lcl|NCBI__GCF_900100495.1:WP_090447968.1 693 FDYPNEIGPGVYDIHSPRVPDSVEMARLLRKAARRIPAERLWVNPDCGLKTRAWAETEAALVNMVAAAR 761
77******************************************************************* PP
TIGR01371 750 elRe 753
+lR
lcl|NCBI__GCF_900100495.1:WP_090447968.1 762 QLRG 765
*995 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (768 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 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 12.62
//
[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