Alignments for a candidate for mmsB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Burkholderia phytofirmans PsJN

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate BPHYT_RS28025 BPHYT_RS28025 3-hydroxyisobutyrate dehydrogenase

Query= reanno::psRCH2:GFF2390
         (296 letters)



>FitnessBrowser__BFirm:BPHYT_RS28025
          Length = 304

 Score =  400 bits (1028), Expect = e-116
 Identities = 202/295 (68%), Positives = 237/295 (80%), Gaps = 1/295 (0%)

Query: 1   MHIGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAEL 60
           M IGFIGLGNMGAPMAHNLLKAGH ++VFDLNA AV+ LV AGA    SP A A  +AE 
Sbjct: 1   MKIGFIGLGNMGAPMAHNLLKAGHAVNVFDLNAQAVQALVDAGAKAAASPKA-AVTDAEC 59

Query: 61  IITMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAP 120
           +ITMLPAAAHV+ V    +G+ A    GV +ID STIDP S +  A+ A +HGN  +DAP
Sbjct: 60  VITMLPAAAHVRSVLSADDGVFAGIAKGVTIIDSSTIDPASVKAFAELAQQHGNTFVDAP 119

Query: 121 VSGGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGI 180
           VSGGTGGAAAGTLTFMVGGS   ++  +P+LAAMGKNIVHCG  G GQVAK+ NN++LGI
Sbjct: 120 VSGGTGGAAAGTLTFMVGGSASAYEQVKPVLAAMGKNIVHCGDTGTGQVAKICNNLVLGI 179

Query: 181 SMIGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFG 240
           +M GVAEAM+LG ALG+DAK L G+INTS+GRCWSSDTYNP PGV++  PS+RGY+GGFG
Sbjct: 180 TMAGVAEAMSLGEALGIDAKVLGGIINTSTGRCWSSDTYNPMPGVIETAPSTRGYTGGFG 239

Query: 241 SDLMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAIINQYRKD 295
           +DLMLKDLGLAT+AAK  RQPV LGALAQQLYQ+ SA+G G LDFSA+I  YR+D
Sbjct: 240 TDLMLKDLGLATDAAKTARQPVYLGALAQQLYQTMSAKGAGRLDFSAVIKLYRQD 294


Lambda     K      H
   0.318    0.134    0.392 

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: 378
Number of extensions: 17
Number of successful extensions: 2
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: 296
Length of database: 304
Length adjustment: 27
Effective length of query: 269
Effective length of database: 277
Effective search space:    74513
Effective search space used:    74513
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS28025 BPHYT_RS28025 (3-hydroxyisobutyrate dehydrogenase)
to HMM TIGR01692 (mmsB: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31))

# 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.carbon/TIGR01692.hmm
# target sequence database:        /tmp/gapView.23467.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01692  [M=288]
Accession:   TIGR01692
Description: HIBADH: 3-hydroxyisobutyrate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   6.8e-145  467.8  12.8   7.7e-145  467.6  12.8    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS28025  BPHYT_RS28025 3-hydroxyisobutyra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS28025  BPHYT_RS28025 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.6  12.8  7.7e-145  7.7e-145       1     288 []       5     292 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 467.6 bits;  conditional E-value: 7.7e-145
                                TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesvy 70 
                                              fiGlGnmG+pma+nllkaghav+vfdl+a+av+ lv+aGa+aaas+++av++a++vitmlPa++hv+sv+
  lcl|FitnessBrowser__BFirm:BPHYT_RS28025   5 FIGLGNMGAPMAHNLLKAGHAVNVFDLNAQAVQALVDAGAKAAASPKAAVTDAECVITMLPAAAHVRSVL 74 
                                              9********************************************************************* PP

                                TIGR01692  71 agdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaeefa 140
                                              ++d+g+ a ++k++ +idsstid+ s ++ ae+a+++G++f+daPvsGG+gga+aGtltfmvGg+a++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS28025  75 SADDGVFAGIAKGVTIIDSSTIDPASVKAFAELAQQHGNTFVDAPVSGGTGGAAAGTLTFMVGGSASAYE 144
                                              ********************************************************************** PP

                                TIGR01692 141 raepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGrcWs 210
                                              +++pvl+amgknivh+Gd+G+Gq+akiCnnl+lgi+m+Gvaea++lge+lG+d+kvl+ i+++s+GrcWs
  lcl|FitnessBrowser__BFirm:BPHYT_RS28025 145 QVKPVLAAMGKNIVHCGDTGTGQVAKICNNLVLGITMAGVAEAMSLGEALGIDAKVLGGIINTSTGRCWS 214
                                              ********************************************************************** PP

                                TIGR01692 211 ldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgagkkdf 280
                                              +dtynP+PGv+e+aP+ +gy+gGf+t+lmlkdlgla +aak+++++v+lGala++ly+++++kgag++df
  lcl|FitnessBrowser__BFirm:BPHYT_RS28025 215 SDTYNPMPGVIETAPSTRGYTGGFGTDLMLKDLGLATDAAKTARQPVYLGALAQQLYQTMSAKGAGRLDF 284
                                              ********************************************************************** PP

                                TIGR01692 281 savikllr 288
                                              savikl+r
  lcl|FitnessBrowser__BFirm:BPHYT_RS28025 285 SAVIKLYR 292
                                              *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (304 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.48
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources