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 Probable 3-hydroxyisobutyrate dehydrogenase; HIBADH; EC 1.1.1.31 (uncharacterized)
to candidate AZOBR_RS26815 AZOBR_RS26815 3-hydroxyisobutyrate dehydrogenase

Query= curated2:P63936
         (294 letters)



>FitnessBrowser__azobra:AZOBR_RS26815
          Length = 299

 Score =  286 bits (733), Expect = 3e-82
 Identities = 152/295 (51%), Positives = 188/295 (63%), Gaps = 4/295 (1%)

Query: 1   MTTIAFLGLGNMGAPMSANLVGAGHVVRGFDPAPTAASGAAAHGVAVFRSAPEAVAEADV 60
           M  IAF+GLGNMG PM  NL  AGH V G+D  P A    AA G  V  +  EA+A+AD 
Sbjct: 1   MARIAFIGLGNMGRPMCDNLTKAGHDVVGYDVVPAARDAYAAAGGRVASTLAEALADADT 60

Query: 61  VITMLPTGEVVRRCYTD---VLAAARPATLFIDSSTISVTDAREVHALAESHGMLQLDAP 117
           VI+M+PTG+ VR  Y D   VLA ARP T+ ID STI V  AR V   A   G + +DAP
Sbjct: 61  VISMIPTGKHVRAAYEDEGGVLAHARPGTMLIDCSTIDVESARAVSKAAADAGFVMVDAP 120

Query: 118 VSGGVKGAAAATLAFMVGGDESTLRRARPVLEPMAGKIIHCGAAGAGQAAKVCNNMVLAV 177
           VSG V  A A TL FMVGG      RARPVL  M  KI H GA+G G A K+CNNM+  +
Sbjct: 121 VSGAVPAAQAGTLTFMVGGTAEGFERARPVLTAMGPKIFHVGASGNGVALKICNNMMAGM 180

Query: 178 QQIAIAEAFVLAEKLGLSAQSLFDVITGATGNCWAVHTNCPVPGPVPTSPANNDFKPGFS 237
             +AI+E F LAEKLGL  Q+++DV+T ++GNCWA+ + CPVPGPVP SPAN D++PGF+
Sbjct: 181 SMVAISEVFALAEKLGLDHQTVYDVMTVSSGNCWALQSYCPVPGPVPASPANRDYQPGFA 240

Query: 238 TALMNKDLGLAMDAVAATGATAPLGSHAADIYAKFAA-DHADLDFSAVIHTLRAR 291
            A+M KD+ L+ +A A +GA  PL   AA +Y       H + DFSAV   +  R
Sbjct: 241 AAMMLKDMRLSQNAAATSGAATPLAGSAAALYQMLVEHGHGNKDFSAVFALITGR 295


Lambda     K      H
   0.319    0.131    0.382 

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: 288
Number of extensions: 9
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: 294
Length of database: 299
Length adjustment: 26
Effective length of query: 268
Effective length of database: 273
Effective search space:    73164
Effective search space used:    73164
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: 48 (23.1 bits)

Align candidate AZOBR_RS26815 AZOBR_RS26815 (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.4373.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-117  376.0  10.7   7.1e-117  375.8  10.7    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS26815  AZOBR_RS26815 3-hydroxyisobutyra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS26815  AZOBR_RS26815 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  375.8  10.7  7.1e-117  7.1e-117       1     286 [.       6     291 ..       6     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 375.8 bits;  conditional E-value: 7.1e-117
                                 TIGR01692   1 fiGlGnmGgpmaanllkaghavrvfdlsakaveelveaGaqaaasaaeaveeadvvitmlPagkhvesv 69 
                                               fiGlGnmG pm  nl kagh v  +d+ ++a +   +aG ++a++ aea ++ad+vi+m+P+gkhv++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS26815   6 FIGLGNMGRPMCDNLTKAGHDVVGYDVVPAARDAYAAAGGRVASTLAEALADADTVISMIPTGKHVRAA 74 
                                               9******************************************************************** PP

                                 TIGR01692  70 yagdegilakvkkksllidsstidvdsarkvaeeaaakGavfldaPvsGGvggaraGtltfmvGgeaee 138
                                               y  + g+la+++ +++lid+stidv+sar+v+++aa++G+v++daPvsG v +a+aGtltfmvGg+ae 
  lcl|FitnessBrowser__azobra:AZOBR_RS26815  75 YEDEGGVLAHARPGTMLIDCSTIDVESARAVSKAAADAGFVMVDAPVSGAVPAAQAGTLTFMVGGTAEG 143
                                               **99***************************************************************** PP

                                 TIGR01692 139 faraepvleamgknivhaGdaGaGqaakiCnnlllgismiGvaealalgeklGldpkvlaeilskssGr 207
                                               f+ra+pvl+amg +i+h+G++G G a kiCnn++ g+sm+ ++e +al+eklGld++++ +++  ssG+
  lcl|FitnessBrowser__azobra:AZOBR_RS26815 144 FERARPVLTAMGPKIFHVGASGNGVALKICNNMMAGMSMVAISEVFALAEKLGLDHQTVYDVMTVSSGN 212
                                               ********************************************************************* PP

                                 TIGR01692 208 cWsldtynPvPGvveqaPasngykgGfatalmlkdlglaqeaaksvkasvllGalarelyslfaskgag 276
                                               cW+l++y+PvPG+v+++Pa+++y++Gfa+a+mlkd++l+q+aa++ +a ++l   a +ly++  ++g+g
  lcl|FitnessBrowser__azobra:AZOBR_RS26815 213 CWALQSYCPVPGPVPASPANRDYQPGFAAAMMLKDMRLSQNAAATSGAATPLAGSAAALYQMLVEHGHG 281
                                               ********************************************************************* PP

                                 TIGR01692 277 kkdfsavikl 286
                                               +kdfsav+ l
  lcl|FitnessBrowser__azobra:AZOBR_RS26815 282 NKDFSAVFAL 291
                                               *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (288 nodes)
Target sequences:                          1  (299 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: 9.10
//
[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