Alignments for a candidate for mmsB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Cupriavidus basilensis 4G11

Align 3-hydroxyisobutyrate dehydrogenase subunit (EC 1.1.1.31) (characterized)
to candidate RR42_RS25325 RR42_RS25325 3-hydroxyisobutyrate dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS25325
          Length = 293

 Score =  311 bits (798), Expect = 9e-90
 Identities = 155/292 (53%), Positives = 210/292 (71%)

Query: 1   MRIAFIGLGNMGAPMARNLIKAGHQLNLFDLNKTVLAELAELGGQISPSPKDAAANSELV 60
           M+I FIGLG+MG PMA NL+++G+ +++FD +   +    E G   + S  D AA  ++V
Sbjct: 1   MKIGFIGLGHMGLPMASNLLRSGNAVHVFDTSSQAIGLAVERGAIATGSIADLAAAVDVV 60

Query: 61  ITMLPAAAHVRSVYLNDDGVLAGIRPGTPTVDCSTIDPQTARDVSKAAAAKGVDMGDAPV 120
           ITMLP  A VRSV    DGVLA  + GT  ++CST DPQTARD+   A + G  M DAPV
Sbjct: 61  ITMLPNPAIVRSVVAGPDGVLAHAKDGTLIIECSTSDPQTARDLESMAQSSGKAMIDAPV 120

Query: 121 SGGTGGAAAGTLTFMVGASAELFASLKPVLEQMGRNIVHCGEVGTGQIAKICNNLLLGIS 180
           SGG  GA AGTLTFMVG + E F + +P+L  MG+NIV+CG  G+GQ AKICNNLLLG+S
Sbjct: 121 SGGVPGAEAGTLTFMVGGTEEAFVAARPILMAMGKNIVNCGPAGSGQAAKICNNLLLGVS 180

Query: 181 MIGVSEAMALGNALGIDTKVLAGIINSSTGRCWSSDTYNPWPGIIETAPASRGYTGGFGA 240
            I VSE+M LG +LG+   VLA IIN+S+GRCW S+ YNP+PG++++APAS  ++GGF  
Sbjct: 181 TIAVSESMCLGVSLGLAPDVLAAIINTSSGRCWVSEVYNPYPGVVKSAPASNDFSGGFAC 240

Query: 241 ELMLKDLGLATEAARQAHQPVILGAVAQQLYQAMSLRGEGGKDFSAIVEGYR 292
           +LM+KDL LA +AA    QP+ + A+++QL+Q +SL+GEG KD +AIV+ ++
Sbjct: 241 DLMIKDLSLALDAASGTRQPLPMTALSKQLFQLLSLKGEGSKDITAIVQMFK 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: 272
Number of extensions: 8
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: 293
Length adjustment: 26
Effective length of query: 269
Effective length of database: 267
Effective search space:    71823
Effective search space used:    71823
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 RR42_RS25325 RR42_RS25325 (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.26873.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-113  365.1   7.2   1.5e-113  364.9   7.2    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS25325  RR42_RS25325 3-hydroxyisobutyrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS25325  RR42_RS25325 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.9   7.2  1.5e-113  1.5e-113       1     287 [.       5     291 ..       5     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 364.9 bits;  conditional E-value: 1.5e-113
                                 TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 
                                               fiGlG mG pma nll++g av+vfd s++a+  +ve Ga a+ s a+ ++ +dvvitmlP  + v+sv
  lcl|FitnessBrowser__Cup4G11:RR42_RS25325   5 FIGLGHMGLPMASNLLRSGNAVHVFDTSSQAIGLAVERGAIATGSIADLAAAVDVVITMLPNPAIVRSV 73 
                                               9******************************************************************** PP

                                 TIGR01692  70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138
                                                ag +g+la++k ++l+i++st d+++ar +   a++ G+ ++daPvsGGv ga+aGtltfmvGg++e+
  lcl|FitnessBrowser__Cup4G11:RR42_RS25325  74 VAGPDGVLAHAKDGTLIIECSTSDPQTARDLESMAQSSGKAMIDAPVSGGVPGAEAGTLTFMVGGTEEA 142
                                               ********************************************************************* PP

                                 TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207
                                               f +a+p+l amgkniv +G aG+GqaakiCnnlllg+s i v+e++ lg+ lGl+p+vla i+++ssGr
  lcl|FitnessBrowser__Cup4G11:RR42_RS25325 143 FVAARPILMAMGKNIVNCGPAGSGQAAKICNNLLLGVSTIAVSESMCLGVSLGLAPDVLAAIINTSSGR 211
                                               ********************************************************************* PP

                                 TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276
                                               cW ++ ynP+PGvv++aPasn+++gGfa +lm kdl la +aa  +++++++ al+++l++l + kg g
  lcl|FitnessBrowser__Cup4G11:RR42_RS25325 212 CWVSEVYNPYPGVVKSAPASNDFSGGFACDLMIKDLSLALDAASGTRQPLPMTALSKQLFQLLSLKGEG 280
                                               ********************************************************************* PP

                                 TIGR01692 277 kkdfsavikll 287
                                                kd +a+++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS25325 281 SKDITAIVQMF 291
                                               ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (293 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: 00:00:00.01
# Mc/sec: 6.67
//
[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