GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Herbaspirillum seropedicae SmR1

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate HSERO_RS06965 HSERO_RS06965 alcohol dehydrogenase

Query= metacyc::MONOMER-12746
         (434 letters)



>FitnessBrowser__HerbieS:HSERO_RS06965
          Length = 422

 Score =  292 bits (748), Expect = 1e-83
 Identities = 172/406 (42%), Positives = 230/406 (56%), Gaps = 18/406 (4%)

Query: 15  AAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMETPIGVIYSTNITPDK 74
           AA  A +  +Q  + QG+YLARAG+C+ACHTA+ G P+AGG  + +P G +Y++NITPDK
Sbjct: 28  AATPAPDPTRQ--LAQGQYLARAGNCMACHTARGGAPYAGGRAIASPFGTLYTSNITPDK 85

Query: 75  T-GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGVAPVAR 133
           T GIG +S +DF +A+ HG  K G  LYPA P+ SY R+S AD  AL+AY ++ + PVAR
Sbjct: 86  TTGIGQWSADDFWRALHHGRGKEGQFLYPAFPYTSYTRLSRADSDALFAY-LQSLPPVAR 144

Query: 134 DNQDSDIPWPLSMRWPLSIWRWM-FAPSVETPAPAAGSDPVISRGAYLVEGLGHCGACHT 192
            NQ   + +P   R  L +WR + F P    P P    D   +RGAYLV+G GHC ACH+
Sbjct: 145 ANQAHTLRFPYDQRMLLGLWRALYFTPQSYQPDPR--QDAQWNRGAYLVQGAGHCSACHS 202

Query: 193 PR-ALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWSEEQLVQFLKTGRS 251
            R  L    + L+ +GG        P   W A  L G   DGL  WS   +   LKTG S
Sbjct: 203 ARNRLGASIEPLALAGGV------IPALQWYAPPLHGG-ADGLQDWSTADIAALLKTGVS 255

Query: 252 DRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQYDKQVAQALWNGDD 311
             +   G MS++V  S+QY+ DAD++A+A YLKSLPA+   D       + A+A      
Sbjct: 256 PHAVTLGPMSEIVGRSLQYLNDADVSAMAVYLKSLPASAADDAARPASVEPAEA---ERI 312

Query: 312 SKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHIVLKGGTLPATHSA 371
            K G  +Y   C  CH   G G    +P LAGN  +      + +  VL GG  P+T   
Sbjct: 313 MKQGKQLYGTLCVDCHGGKGQGSAPDYPPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGN 372

Query: 372 PSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALRN 417
           P  F MP F  +LSDQEVA VV+++R+SWGNQ   V   +V   R+
Sbjct: 373 PYPFGMPPFGPQLSDQEVAAVVSYVRNSWGNQGGLVSAAEVNRYRS 418


Lambda     K      H
   0.316    0.131    0.404 

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: 660
Number of extensions: 47
Number of successful extensions: 10
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: 434
Length of database: 422
Length adjustment: 32
Effective length of query: 402
Effective length of database: 390
Effective search space:   156780
Effective search space used:   156780
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: 51 (24.3 bits)

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