Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate WP_011913953.1 PST_RS14290 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Query= BRENDA::P25665
(753 letters)
>NCBI__GCF_000013785.1:WP_011913953.1
Length = 771
Score = 913 bits (2360), Expect = 0.0
Identities = 463/760 (60%), Positives = 561/760 (73%), Gaps = 15/760 (1%)
Query: 6 HTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVGDFA 65
H LGFPR+G RELKKA E+YW G + L VGR+LRARHW Q AGI+LLPVGDFA
Sbjct: 5 HNLGFPRIGADRELKKALEAYWKGELDEQGLRQVGRQLRARHWQAQLDAGIELLPVGDFA 64
Query: 66 WYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTG-EPAAAAEMTKWFNTNYH 124
WYD VL+ SL+ G +P R + +G +DTLF + RG A + A A EMTKWF+TNYH
Sbjct: 65 WYDQVLSHSLMFGVIPQRFRPAEGQATLDTLFAMARGVARSCCGGAQAQEMTKWFDTNYH 124
Query: 125 YMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPVTWLWLGKVKGEQ-----FD 179
Y+VPEF QQF+L+WTQL +EV+EA ALGH +KPVL+GP+++LWLGK+KGE FD
Sbjct: 125 YLVPEFSVDQQFQLSWTQLFEEVEEAKALGHAIKPVLIGPLSYLWLGKLKGEADQTQTFD 184
Query: 180 RLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAYKPAYDALQ-GQVKL 238
+L LL+ +LPVY +VL LA +G+EWVQIDEP L L+LPQ W +A++ AY+ LQ +K
Sbjct: 185 KLELLDRLLPVYGEVLDRLAAQGVEWVQIDEPILALDLPQDWKNAFERAYNLLQRAPLKK 244
Query: 239 LLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDWLLSAGLINGRNVWR 298
L+ TYF G+ NL LPV GLH+DLV + + RLP+ +LS GL+NGRNVWR
Sbjct: 245 LVATYFGGLEDNLGLAATLPVDGLHIDLVRAPEQYPVILDRLPAYKVLSLGLVNGRNVWR 304
Query: 299 ADLT---EKYAQIKDIVGKRDLWVASSCSLLHSPIDLSVETRLDAEVKSWFAFALQKCHE 355
DL E + +G+R LW+A SCSLLHSP+DL E RLD EVKSW AFA+QKC E
Sbjct: 305 CDLDKALEVARHAAERLGER-LWLAPSCSLLHSPVDLEREDRLDEEVKSWLAFAVQKCSE 363
Query: 356 LALLRDALNSGDTA----ALAEWSAPIQARRHSTRVHNPAVEKRLAAITAQDSQRANVYE 411
+A L A++ A ALA A AR S R+H PAV+ RLAAI A+DS+R +V+
Sbjct: 364 VATLARAIDDPQDAEVQAALARSRAVQAARAQSPRIHKPAVQARLAAIEAKDSRRTSVFA 423
Query: 412 VRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRTGIAEHIKQAIVE 471
R E QRAR +LPA+PTTTIGSFPQT IR R +K+G L +Y + I+ A+
Sbjct: 424 TRIELQRARLQLPAFPTTTIGSFPQTPAIRLARQAYKQGRLSLGDYTEAMQAEIRHAVAV 483
Query: 472 QERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKPPIVIGDISRPAP 531
QE++GLDVLVHGEAERNDMVEYF E L+G+VFT+ GWVQSYGSRCVKP I+ GD+SRP P
Sbjct: 484 QEQIGLDVLVHGEAERNDMVEYFAEQLEGYVFTRFGWVQSYGSRCVKPAIIYGDLSRPRP 543
Query: 532 ITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIALALRDEVADLEAA 591
+TV+W +YAQ TD+ +KGMLTGPVT+L WSF REDV RE A+Q+ALA+RDEV DLEAA
Sbjct: 544 MTVDWIRYAQQQTDRIMKGMLTGPVTMLMWSFAREDVPREVQARQLALAIRDEVCDLEAA 603
Query: 592 GIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIHTHMCYCEFNDIM 651
GI IIQIDE A REGLPLRR W YL W VEAFR+ A+ +D+TQIHTHMCY EFND++
Sbjct: 604 GIRIIQIDEAAFREGLPLRREQWRHYLDWAVEAFRLCASGVRDETQIHTHMCYSEFNDVI 663
Query: 652 DSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVPSVEWIEALLKKA 711
+SIAA+DADVITIETSRS MELLE+F FDYPN+IGPGVYDIHSP VP + LL+KA
Sbjct: 664 ESIAAMDADVITIETSRSQMELLEAFRAFDYPNDIGPGVYDIHSPRVPDTAEMVQLLEKA 723
Query: 712 AKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
A+ IPAERLWVNPDCGLKTRGWPET AAL NMV AA+ LR
Sbjct: 724 AECIPAERLWVNPDCGLKTRGWPETEAALVNMVAAARQLR 763
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: 1679
Number of extensions: 68
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: 771
Length adjustment: 40
Effective length of query: 713
Effective length of database: 731
Effective search space: 521203
Effective search space used: 521203
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_011913953.1 PST_RS14290 (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.1190.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 1095.5 0.0 0 1095.3 0.0 1.0 1 lcl|NCBI__GCF_000013785.1:WP_011913953.1 PST_RS14290 5-methyltetrahydropt
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013785.1:WP_011913953.1 PST_RS14290 5-methyltetrahydropteroyltriglutamate--homocysteine methyltrans
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1095.3 0.0 0 0 1 753 [. 7 764 .. 7 765 .. 0.97
Alignments for each domain:
== domain 1 score: 1095.3 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDhvLdtavl 69
lgfPrig+ Relkkale+ywkg+++++ l +v ++lr++++++q +ag++++pv+df++YD+vL +++
lcl|NCBI__GCF_000013785.1:WP_011913953.1 7 LGFPRIGADRELKKALEAYWKGELDEQGLRQVGRQLRARHWQAQLDAGIELLPVGDFAWYDQVLSHSLM 75
79******************************************************************* PP
TIGR01371 70 lgaiperfkeladdesdldtyFaiaRGtek...kdvaalemtkwfntnYhYlvPelskeeefklsknkl 135
+g+ip+rf+ +++ ++ldt+Fa+aRG ++ +++a+emtkwf+tnYhYlvPe+s +++f+ls+++l
lcl|NCBI__GCF_000013785.1:WP_011913953.1 76 FGVIPQRFRPAEGQ-ATLDTLFAMARGVARsccGGAQAQEMTKWFDTNYHYLVPEFSVDQQFQLSWTQL 143
**********9555.68***********99888899********************************* PP
TIGR01371 136 leeykeakelgvetkPvllGpitflkLakakee....eekellellekllpvYkevlkklaeagvewvq 200
+ee++eak+lg+ kPvl+Gp+++l+L+k k e +++++lell++llpvY evl++la++gvewvq
lcl|NCBI__GCF_000013785.1:WP_011913953.1 144 FEEVEEAKALGHAIKPVLIGPLSYLWLGKLKGEadqtQTFDKLELLDRLLPVYGEVLDRLAAQGVEWVQ 212
****************************9887655556788999************************* PP
TIGR01371 201 idePvlvldlskeelaavkeayeeleeaskelklllqtYfdsveealeklvslpvealglDlveakeel 269
ideP+l+ldl++++++a+++ay+ l++ + lk l++tYf+ +e++l ++ lpv++l++Dlv+a+e+
lcl|NCBI__GCF_000013785.1:WP_011913953.1 213 IDEPILALDLPQDWKNAFERAYNLLQR--APLKKLVATYFGGLEDNLGLAATLPVDGLHIDLVRAPEQY 279
*************************97..4777789********************************* PP
TIGR01371 270 elakakfeedkvLvaGvidGrniwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldk 338
+ ++++ kvL++G+++Grn+w+ dl k+l++ ++ +++ g++l++++scsllh+pvdle+e++ld+
lcl|NCBI__GCF_000013785.1:WP_011913953.1 280 PVILDRLPAYKVLSLGLVNGRNVWRCDLDKALEVARHAAERLGERLWLAPSCSLLHSPVDLEREDRLDE 348
********************************************************************* PP
TIGR01371 339 elkellafakekleelkvlkealeg..eaavaealeaeaaaiaarkkskrvadekvkerlealkekkar 405
e+k++lafa++k++e+++l++a+++ +a+v++al+ ++a aar++s+r+++ +v++rl+a+++k++r
lcl|NCBI__GCF_000013785.1:WP_011913953.1 349 EVKSWLAFAVQKCSEVATLARAIDDpqDAEVQAALARSRAVQAARAQSPRIHKPAVQARLAAIEAKDSR 417
************************99444555566666666678999********************** PP
TIGR01371 406 ressfeeRaeaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqee 474
r+s f++R e q+++l+lP++PtttiGsfPqt +R aR+++++g++s +Y++++++ei++++++qe+
lcl|NCBI__GCF_000013785.1:WP_011913953.1 418 RTSVFATRIELQRARLQLPAFPTTTIGSFPQTPAIRLARQAYKQGRLSLGDYTEAMQAEIRHAVAVQEQ 486
********************************************************************* PP
TIGR01371 475 lglDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkeskyaqsl 543
+glDvLvhGe+eRnDmveyF+e+l+G++ft++gWvqsYGsRcvkP+iiygd+srp+pmtv++++yaq
lcl|NCBI__GCF_000013785.1:WP_011913953.1 487 IGLDVLVHGEAERNDMVEYFAEQLEGYVFTRFGWVQSYGSRCVKPAIIYGDLSRPRPMTVDWIRYAQQQ 555
********************************************************************* PP
TIGR01371 544 tskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDepalReglPlrks 612
t++ +kGmLtGPvt+l Wsf ReD+pr+ +a+q+ala+rdev dLe+agi+iiqiDe+a+ReglPlr++
lcl|NCBI__GCF_000013785.1:WP_011913953.1 556 TDRIMKGMLTGPVTMLMWSFAREDVPREVQARQLALAIRDEVCDLEAAGIRIIQIDEAAFREGLPLRRE 624
********************************************************************* PP
TIGR01371 613 dkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvisieasrsdmelldalkeik 681
++++YldwaveaFrl asgv+detqihthmCYsefn++ie+iaa+daDvi+ie+srs+mell+a+++ +
lcl|NCBI__GCF_000013785.1:WP_011913953.1 625 QWRHYLDWAVEAFRLCASGVRDETQIHTHMCYSEFNDVIESIAAMDADVITIETSRSQMELLEAFRA-F 692
*******************************************************************.7 PP
TIGR01371 682 kyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvnPDCGLktRkweevkaalknlveaake 750
+y+++iG+GvyDihsprvP + e+ +lleka + +p+erlWvnPDCGLktR w+e++aal n+v+aa++
lcl|NCBI__GCF_000013785.1:WP_011913953.1 693 DYPNDIGPGVYDIHSPRVPDTAEMVQLLEKAAECIPAERLWVNPDCGLKTRGWPETEAALVNMVAAARQ 761
7******************************************************************** PP
TIGR01371 751 lRe 753
lR+
lcl|NCBI__GCF_000013785.1:WP_011913953.1 762 LRA 764
*97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (771 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 13.16
//
[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