Align 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC 2.1.1.14) (characterized)
to candidate Ac3H11_2345 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14)
Query= BRENDA::P25665
(753 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_2345
Length = 810
Score = 854 bits (2207), Expect = 0.0
Identities = 442/772 (57%), Positives = 536/772 (69%), Gaps = 23/772 (2%)
Query: 3 ILNHTLGFPRVGLRRELKKAQESYWAGNSTREELLAVGRELRARHWDQQKQAGIDLLPVG 62
+L HTLGFPR+G +R LK A ES+W G+ST +L A +LR +HW Q AG+ + VG
Sbjct: 30 VLTHTLGFPRMGAQRALKFALESFWRGDSTEADLQATAAQLRQQHWQAQADAGLGCVTVG 89
Query: 63 DFAWYDHVLTTSLLLGNVPARHQNKDGSVDIDTLFRIGRGRAPTGEP------------- 109
DFA YDHV LLG PAR + ++ F + RG + P
Sbjct: 90 DFALYDHVANHIQLLGCEPARFGFDAHTPELARYFAMARGVSAHTTPDHAGCSAGCTAKH 149
Query: 110 ----AAAAEMTKWFNTNYHYMVPEFVKGQQFKLTWTQLLDEVDEALALGHKVKPVLLGPV 165
A EMTKWF+TNYHY+VPEF QF L +L EV EALALGH+VK VLLGP+
Sbjct: 150 HTAGQPALEMTKWFDTNYHYLVPEFSAHTQFHLASERLFAEVAEALALGHRVKAVLLGPL 209
Query: 166 TWLWLGKVKGEQFDRLSLLNDILPVYQQVLAELAKRGIEWVQIDEPALVLELPQAWLDAY 225
++LWLGK K FDR SLL +LPVY+ VLA L +G+EWVQIDEP L L+LP AW A+
Sbjct: 210 SFLWLGKSKTAGFDRFSLLESLLPVYEAVLARLKAQGVEWVQIDEPILGLDLPDAWRHAF 269
Query: 226 KPAYDAL-QGQVKLLLTTYFEGVTPNLDTITALPVQGLHVDLVHGKDDVAELHKRLPSDW 284
+P+Y L + KLLL TYF + NL LPV GLHVD V D++ + LPS
Sbjct: 270 EPSYWQLARSAPKLLLATYFSPLAENLRLACQLPVAGLHVDAVRAPDELVGVADWLPSHK 329
Query: 285 LLSAGLINGRNVWRADLTEKYAQIKDIVGKR--DLWVASSCSLLHSPIDLSVETRLDAEV 342
+LS G+++GRN+WR DL +++ + K +LW+A SCSLLH P L ET+LDAEV
Sbjct: 330 VLSVGIVDGRNIWRTDLDTALQKLRPVADKHQGELWLAPSCSLLHVPFSLEAETQLDAEV 389
Query: 343 KSWFAFALQKCHELALLRDALNSGDTAALAEWSAP---IQARRHSTRVHNPAVEKRLAAI 399
KSW AFA++K EL +L AL+ G+ A E A + ARR S RVH V R+AA
Sbjct: 390 KSWLAFAVEKLDELRVLSTALSQGEAAVDDELHAARTALAARRASPRVHRATVAARIAAA 449
Query: 400 TAQDSQRANVYEVRAEAQRARFKLPAWPTTTIGSFPQTTEIRTLRLDFKKGNLDANNYRT 459
QRA+ + R +AQRAR KLP PTTTIGSFPQT EIR R FK+G LD+ +Y+
Sbjct: 450 APGADQRASAFPARQKAQRARLKLPLLPTTTIGSFPQTAEIRAARAAFKRGALDSTHYQQ 509
Query: 460 GIAEHIKQAIVEQERLGLDVLVHGEAERNDMVEYFGEHLDGFVFTQNGWVQSYGSRCVKP 519
+ I+ A+ +QE LGLDVLVHGEAERNDMVEYFGE LDGF FT NGWVQSYGSRCVKP
Sbjct: 510 KMQAEIELAVRKQEALGLDVLVHGEAERNDMVEYFGEQLDGFAFTANGWVQSYGSRCVKP 569
Query: 520 PIVIGDISRPAPITVEWAKYAQSLTDKPVKGMLTGPVTILCWSFPREDVSRETIAKQIAL 579
PI+ GD++RP P+TV W +YAQSLT KP+KGMLTGP+TIL WSF R+D R T A QIA
Sbjct: 570 PIIYGDVARPTPMTVAWTQYAQSLTTKPMKGMLTGPITILQWSFVRDDQPRATTADQIAW 629
Query: 580 ALRDEVADLEAAGIGIIQIDEPALREGLPLRRSDWDAYLQWGVEAFRINAAVAKDDTQIH 639
A+RDEV DLEAA I IIQIDEPA+REGLPLRR+ W +YL AFRI+A+ ++DTQIH
Sbjct: 630 AIRDEVCDLEAADIAIIQIDEPAIREGLPLRRAGWKSYLDRATRAFRISASGVRNDTQIH 689
Query: 640 THMCYCEFNDIMDSIAALDADVITIETSRSDMELLESFEEFDYPNEIGPGVYDIHSPNVP 699
THMCY EFNDI+ +IAA+DADVITIETSRSDMELL+ F +F YPNEIGPGVYDIHSP VP
Sbjct: 690 THMCYSEFNDILPAIAAMDADVITIETSRSDMELLQGFGDFRYPNEIGPGVYDIHSPRVP 749
Query: 700 SVEWIEALLKKAAKRIPAERLWVNPDCGLKTRGWPETRAALANMVQAAQNLR 751
V+ + ALL+KAA+ +P E LWVNPDCGLKTRGWPET AAL +MVQAA+ +R
Sbjct: 750 GVQEMAALLEKAAEVVPVEHLWVNPDCGLKTRGWPETEAALRHMVQAAREVR 801
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: 1684
Number of extensions: 76
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: 810
Length adjustment: 41
Effective length of query: 712
Effective length of database: 769
Effective search space: 547528
Effective search space used: 547528
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 Ac3H11_2345 (5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (EC 2.1.1.14))
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.9108.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 1058.2 0.0 0 1058.0 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 5-methyltetrahydropteroyltriglut
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransfera
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1058.0 0.0 0 0 1 753 [. 35 802 .. 35 803 .. 0.99
Alignments for each domain:
== domain 1 score: 1058.0 bits; conditional E-value: 0
TIGR01371 1 lgfPrigekRelkkalekywkgkiskeellkvakdlrkkalkkqkeagvdvipvndfslYDh 62
lgfPr+g++R lk+ale++w+g++++++l+++a++lr++++++q++ag+ +++v+df+lYDh
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 35 LGFPRMGAQRALKFALESFWRGDSTEADLQATAAQLRQQHWQAQADAGLGCVTVGDFALYDH 96
79************************************************************ PP
TIGR01371 63 vLdtavllgaiperfkeladdesdldtyFaiaRGtek...................kdvaal 105
v + llg p+rf ++ +l++yFa+aRG + + +al
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 97 VANHIQLLGCEPARFGFD-AHTPELARYFAMARGVSAhttpdhagcsagctakhhtAGQPAL 157
****************97.66679**********99899**************9998899** PP
TIGR01371 106 emtkwfntnYhYlvPelskeeefklsknklleeykeakelgvetkPvllGpitflkLakake 167
emtkwf+tnYhYlvPe+s++++f+l++++l+ e+ ea +lg+ +k vllGp++fl+L+k+k
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 158 EMTKWFDTNYHYLVPEFSAHTQFHLASERLFAEVAEALALGHRVKAVLLGPLSFLWLGKSKT 219
***********************************************************996 PP
TIGR01371 168 eeekellellekllpvYkevlkklaeagvewvqidePvlvldlskeelaavkeayeeleeas 229
+++ +lle+llpvY+ vl +l+++gvewvqideP+l ldl++++++a++ y +l++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 220 -AGFDRFSLLESLLPVYEAVLARLKAQGVEWVQIDEPILGLDLPDAWRHAFEPSYWQLAR-- 278
.88*******************************************************97.. PP
TIGR01371 230 kelklllqtYfdsveealeklvslpvealglDlveakeelelakakfeedkvLvaGvidGrn 291
++ klll+tYf + e+l+ + +lpv++l++D v+a++el ++ ++++kvL++G++dGrn
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 279 SAPKLLLATYFSPLAENLRLACQLPVAGLHVDAVRAPDELVGVADWLPSHKVLSVGIVDGRN 340
799************************************9999999**************** PP
TIGR01371 292 iwkadlekslkllkkleakagdklvvstscsllhvpvdleleekldkelkellafakeklee 353
iw++dl +l++l+ +++k++ +l++++scsllhvp++le+e++ld+e+k++lafa+ekl+e
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 341 IWRTDLDTALQKLRPVADKHQGELWLAPSCSLLHVPFSLEAETQLDAEVKSWLAFAVEKLDE 402
*********************99*************************************** PP
TIGR01371 354 lkvlkealeg.eaavaealeaeaaaiaarkkskrvadekvkerlealkekkarressfeeRa 414
l+vl++al++ eaav ++l+a+++a+aar+ s+rv+ ++v++r++a +r+s f +R+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 403 LRVLSTALSQgEAAVDDELHAARTALAARRASPRVHRATVAARIAAAAPGADQRASAFPARQ 464
*********99*************************************************** PP
TIGR01371 415 eaqekklnlPllPtttiGsfPqtkevRkaRakfrkgeiseeeYekfikeeikkviklqeelg 476
+aq+++l+lPllPtttiGsfPqt+e+R aRa+f++g +++ +Y++ +++ei+ +++ qe+lg
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 465 KAQRARLKLPLLPTTTIGSFPQTAEIRAARAAFKRGALDSTHYQQKMQAEIELAVRKQEALG 526
************************************************************** PP
TIGR01371 477 lDvLvhGefeRnDmveyFgeklaGfaftqngWvqsYGsRcvkPpiiygdvsrpkpmtvkesk 538
lDvLvhGe+eRnDmveyFge+l+Gfaft+ngWvqsYGsRcvkPpiiygdv rp pmtv++++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 527 LDVLVHGEAERNDMVEYFGEQLDGFAFTANGWVQSYGSRCVKPPIIYGDVARPTPMTVAWTQ 588
************************************************************** PP
TIGR01371 539 yaqsltskpvkGmLtGPvtilnWsfvReDlprkeiaeqialalrdevkdLeeagikiiqiDe 600
yaqslt+kp+kGmLtGP+til+WsfvR+D+pr+++a+qia a+rdev dLe+a i+iiqiDe
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 589 YAQSLTTKPMKGMLTGPITILQWSFVRDDQPRATTADQIAWAIRDEVCDLEAADIAIIQIDE 650
************************************************************** PP
TIGR01371 601 palReglPlrksdkeeYldwaveaFrlaasgvkdetqihthmCYsefneiieaiaaldaDvi 662
pa+ReglPlr++ +++Yld a +aFr++asgv+++tqihthmCYsefn+i+ aiaa+daDvi
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 651 PAIREGLPLRRAGWKSYLDRATRAFRISASGVRNDTQIHTHMCYSEFNDILPAIAAMDADVI 712
************************************************************** PP
TIGR01371 663 sieasrsdmelldalkeikkyekeiGlGvyDihsprvPskeelaellekalkklpkerlWvn 724
+ie+srsdmell+ + + ++y++eiG+GvyDihsprvP ++e+a+lleka +++p e+lWvn
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 713 TIETSRSDMELLQGFGD-FRYPNEIGPGVYDIHSPRVPGVQEMAALLEKAAEVVPVEHLWVN 773
*****************.66****************************************** PP
TIGR01371 725 PDCGLktRkweevkaalknlveaakelRe 753
PDCGLktR w+e++aal+++v+aa+e+Re
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2345 774 PDCGLKTRGWPETEAALRHMVQAAREVRE 802
****************************8 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (754 nodes)
Target sequences: 1 (810 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 0.03s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 9.26
//
[ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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