Alignments for a candidate for mmsB in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsB in Azospirillum brasilense Sp245

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate AZOBR_RS22360 AZOBR_RS22360 3-hydroxyisobutyrate dehydrogenase

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



>FitnessBrowser__azobra:AZOBR_RS22360
          Length = 296

 Score =  296 bits (757), Expect = 5e-85
 Identities = 159/291 (54%), Positives = 193/291 (66%), Gaps = 1/291 (0%)

Query: 3   IGFIGLGNMGAPMAHNLLKAGHQLSVFDLNAAAVENLVGAGALPVDSPTAIAQGNAELII 62
           I FIGLGNMGAPM  NLLKAGH +  FDL+ AA      AGA     P A A G AE+++
Sbjct: 4   IAFIGLGNMGAPMMRNLLKAGHTVLAFDLSEAACTAARDAGATIATGPGAAA-GEAEVVV 62

Query: 63  TMLPAAAHVKGVYLGVNGLIAHSRAGVMLIDCSTIDPHSAREVAKAAAEHGNPMLDAPVS 122
           TMLPA  HV+ VY   +G+IA ++ G + ID ST+D  SAR VA AA   G+ M+DAPVS
Sbjct: 63  TMLPAGKHVREVYTAPDGIIAKAKPGSLFIDSSTVDVDSARFVAAAAEAAGHAMVDAPVS 122

Query: 123 GGTGGAAAGTLTFMVGGSDPDFDHAQPILAAMGKNIVHCGAAGNGQVAKVANNMLLGISM 182
           GG GGA A TLTFMVGGSD  F  A+PIL+AMGK IVH G  GNGQ AK+ NNM+LGISM
Sbjct: 123 GGVGGAEAATLTFMVGGSDTAFRRAEPILSAMGKAIVHTGGPGNGQAAKICNNMILGISM 182

Query: 183 IGVAEAMALGVALGMDAKTLAGVINTSSGRCWSSDTYNPFPGVLDNVPSSRGYSGGFGSD 242
           +GV+EA AL   LG+ ++ L  V + SSG+CWS  +Y P PG +   P++R Y  GF + 
Sbjct: 183 LGVSEAFALAEKLGLGSQKLFDVASKSSGQCWSLTSYCPVPGPVPTSPANRDYQPGFAAA 242

Query: 243 LMLKDLGLATEAAKQVRQPVILGALAQQLYQSFSAQGHGGLDFSAIINQYR 293
           LMLKDL LA EA +    P+ LG  A Q+Y  F   G GG DFS I+N  R
Sbjct: 243 LMLKDLKLAVEAGQSTGSPLPLGGEAAQMYALFCNAGFGGKDFSGIVNLLR 293


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: 300
Number of extensions: 14
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: 296
Length adjustment: 26
Effective length of query: 270
Effective length of database: 270
Effective search space:    72900
Effective search space used:    72900
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 AZOBR_RS22360 AZOBR_RS22360 (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.15015.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-134  433.1   8.6   2.9e-134  432.9   8.6    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS22360  AZOBR_RS22360 3-hydroxyisobutyra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS22360  AZOBR_RS22360 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.9   8.6  2.9e-134  2.9e-134       1     288 []       6     293 ..       6     293 .. 1.00

  Alignments for each domain:
  == domain 1  score: 432.9 bits;  conditional E-value: 2.9e-134
                                 TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 
                                               fiGlGnmG+pm +nllkagh+v +fdls +a+  +++aGa++a+ + +a+ ea+vv+tmlPagkhv++v
  lcl|FitnessBrowser__azobra:AZOBR_RS22360   6 FIGLGNMGAPMMRNLLKAGHTVLAFDLSEAACTAARDAGATIATGPGAAAGEAEVVVTMLPAGKHVREV 74 
                                               9******************************************************************** PP

                                 TIGR01692  70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138
                                               y++ +gi+ak+k +sl+idsst+dvdsar va++a+a+G+ ++daPvsGGvgga+a tltfmvGg++ +
  lcl|FitnessBrowser__azobra:AZOBR_RS22360  75 YTAPDGIIAKAKPGSLFIDSSTVDVDSARFVAAAAEAAGHAMVDAPVSGGVGGAEAATLTFMVGGSDTA 143
                                               ********************************************************************* PP

                                 TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207
                                               f+raep+l+amgk ivh+G+ G GqaakiCnn++lgism+Gv+ea+al+eklGl ++ l++++skssG+
  lcl|FitnessBrowser__azobra:AZOBR_RS22360 144 FRRAEPILSAMGKAIVHTGGPGNGQAAKICNNMILGISMLGVSEAFALAEKLGLGSQKLFDVASKSSGQ 212
                                               ********************************************************************* PP

                                 TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276
                                               cWsl++y+PvPG+v+++Pa+++y++Gfa+almlkdl+la ea +s++++++lG  a ++y+lf+++g+g
  lcl|FitnessBrowser__azobra:AZOBR_RS22360 213 CWSLTSYCPVPGPVPTSPANRDYQPGFAAALMLKDLKLAVEAGQSTGSPLPLGGEAAQMYALFCNAGFG 281
                                               ********************************************************************* PP

                                 TIGR01692 277 kkdfsavikllr 288
                                               +kdfs++++llr
  lcl|FitnessBrowser__azobra:AZOBR_RS22360 282 GKDFSGIVNLLR 293
                                               **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (296 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: 11.20
//
[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