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.12669.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.09
//
[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:

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:

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:

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:

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