Alignments for a candidate for mmsB in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Paraburkholderia bryophila 376MFSha3.1

Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate H281DRAFT_01201 H281DRAFT_01201 3-hydroxyisobutyrate dehydrogenase

Query= metacyc::MONOMER-11664
         (295 letters)



>FitnessBrowser__Burk376:H281DRAFT_01201
          Length = 309

 Score =  394 bits (1012), Expect = e-114
 Identities = 197/292 (67%), Positives = 231/292 (79%)

Query: 1   MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELV 60
           M+I FIGLGNMGAPMA NL+KAGH +N+FDLN   +  L + G   + SPK A A+ E V
Sbjct: 1   MKIGFIGLGNMGAPMAHNLLKAGHAVNVFDLNAQAVQALVDAGAHAAASPKAAVADVECV 60

Query: 61  ITMLPAAAHVRSVYLNDDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120
           ITMLPAAAHVRSV   DDGVLAGI  G   VD STIDP + +  ++ A  +G    DAPV
Sbjct: 61  ITMLPAAAHVRSVLTADDGVLAGIPQGVTIVDSSTIDPASVKAFAELAQQRGNTFVDAPV 120

Query: 121 SGGTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180
           SGGTGGAAAGTLTFMVG SA  +  +KPVL  MGRNIVHCG+ GTGQ+AKICNNL+LGI+
Sbjct: 121 SGGTGGAAAGTLTFMVGGSASAYEKVKPVLSAMGRNIVHCGDTGTGQVAKICNNLVLGIT 180

Query: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240
           M GV+EAM+LG ALGID KVLAGIIN+STGRCWSSDTYNP PG+I++AP+SR Y+GGFG 
Sbjct: 181 MAGVAEAMSLGEALGIDVKVLAGIINTSTGRCWSSDTYNPMPGVIDSAPSSREYSGGFGT 240

Query: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYR 292
           +LMLKDLGLAT+AAR A QPV LGA+AQQLYQ MS +G G  DFSA+++ YR
Sbjct: 241 DLMLKDLGLATDAARFARQPVYLGALAQQLYQTMSAKGAGRLDFSAVIKLYR 292


Lambda     K      H
   0.317    0.134    0.386 

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: 353
Number of extensions: 14
Number of successful extensions: 1
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: 295
Length of database: 309
Length adjustment: 27
Effective length of query: 268
Effective length of database: 282
Effective search space:    75576
Effective search space used:    75576
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate H281DRAFT_01201 H281DRAFT_01201 (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.1460.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.9e-143  463.0  10.4   2.2e-143  462.9  10.4    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01201  H281DRAFT_01201 3-hydroxyisobuty


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01201  H281DRAFT_01201 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.9  10.4  2.2e-143  2.2e-143       1     288 []       5     292 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 462.9 bits;  conditional E-value: 2.2e-143
                                    TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhv 66 
                                                  fiGlGnmG+pma+nllkaghav+vfdl+a+av+ lv+aGa+aaas+++av+++++vitmlPa++hv
  lcl|FitnessBrowser__Burk376:H281DRAFT_01201   5 FIGLGNMGAPMAHNLLKAGHAVNVFDLNAQAVQALVDAGAHAAASPKAAVADVECVITMLPAAAHV 70 
                                                  9***************************************************************** PP

                                    TIGR01692  67 esvyagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmv 132
                                                  +sv+++d+g+la + +++ ++dsstid+ s ++ ae+a+++G++f+daPvsGG+gga+aGtltfmv
  lcl|FitnessBrowser__Burk376:H281DRAFT_01201  71 RSVLTADDGVLAGIPQGVTIVDSSTIDPASVKAFAELAQQRGNTFVDAPVSGGTGGAAAGTLTFMV 136
                                                  ****************************************************************** PP

                                    TIGR01692 133 GgeaeefaraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvla 198
                                                  Gg+a+++++++pvl+amg+nivh+Gd+G+Gq+akiCnnl+lgi+m+Gvaea++lge+lG+d kvla
  lcl|FitnessBrowser__Burk376:H281DRAFT_01201 137 GGSASAYEKVKPVLSAMGRNIVHCGDTGTGQVAKICNNLVLGITMAGVAEAMSLGEALGIDVKVLA 202
                                                  ****************************************************************** PP

                                    TIGR01692 199 eilskssGrcWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalar 264
                                                   i+++s+GrcWs+dtynP+PGv+++aP+s++y+gGf+t+lmlkdlgla +aa+ ++++v+lGala+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01201 203 GIINTSTGRCWSSDTYNPMPGVIDSAPSSREYSGGFGTDLMLKDLGLATDAARFARQPVYLGALAQ 268
                                                  ****************************************************************** PP

                                    TIGR01692 265 elyslfaskgagkkdfsavikllr 288
                                                  +ly+++++kgag++dfsavikl+r
  lcl|FitnessBrowser__Burk376:H281DRAFT_01201 269 QLYQTMSAKGAGRLDFSAVIKLYR 292
                                                  ***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (309 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.70
//
[ok]

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

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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