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.6993.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 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 13.20
//
[ok]
This GapMind analysis is from Apr 09 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