GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Acidovorax sp. GW101-3H11

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate Ac3H11_2872 Putative diheme cytochrome c-553

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2872
          Length = 426

 Score =  306 bits (784), Expect = 8e-88
 Identities = 174/411 (42%), Positives = 238/411 (57%), Gaps = 19/411 (4%)

Query: 1   MKALVIATLALLGSAAANAAEADQQ--ALVQQGEYLARAGDCVACHTAKDGKPFAGGLPM 58
           M A  + TL L G     A E  Q   ALVQ+GEYLAR G+C+ACHT + G PFAGG  +
Sbjct: 17  MAAAAVVTLNLRGEEPLPATETLQSTPALVQRGEYLARVGNCMACHTTQGGAPFAGGRGI 76

Query: 59  ETPIGVIYSTNITPDKT-GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADM 117
           ETP GV++S+N+TPDK  GIG ++  +F +A+ HG +K G  LYPA P+P+Y +V+  D 
Sbjct: 77  ETPFGVVHSSNLTPDKAQGIGSWTSAEFWRAMHHGRSKDGRLLYPAFPYPNYTQVTREDS 136

Query: 118 QALYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISRG 177
            A++AY     A VA  N+   + +P + +  L +WR +F  +   P P A      +RG
Sbjct: 137 DAIFAYLQSQPA-VAEPNRAHALRFPYNTQAALGVWRALFF-TPGAPQPEATQSAEYNRG 194

Query: 178 AYLVEGLGHCGACHTPRALTMQEKALSASGGSD-FLSGSAPLEGWIAKSLRGDHKDGLGS 236
           AYLV GLGHC ACHTPR       AL A+  +  F  G  P++ W A +L   H+ G+  
Sbjct: 195 AYLVNGLGHCTACHTPR------NALGATTDAKAFTGGLIPVQNWYAPALNAAHEAGVKE 248

Query: 237 WSEEQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPH 296
           W  + +V  LKTG + + +V G M++VV  S Q+++DAD  A+A YL++LP      Q H
Sbjct: 249 WKTDDVVALLKTGVAPQGSVLGPMAEVVFRSAQHLSDADARAMAVYLQALP-----QQEH 303

Query: 297 QYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLI 356
           +     A A         GA VY  +CA CH   G G    FPALAGN  +  AD T+L+
Sbjct: 304 R--ALAAGAAPPASALARGAKVYEQHCAQCHGDQGQGEPGAFPALAGNRAVTLADPTNLV 361

Query: 357 HIVLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAV 407
            +VL+GG LPAT   P    MP F   LSD+++A V   +R+SWGN+A  V
Sbjct: 362 RVVLQGGYLPATAGNPRPHGMPPFQQLLSDEDIAAVTTLVRNSWGNRAPGV 412


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: 612
Number of extensions: 54
Number of successful extensions: 9
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: 426
Length adjustment: 32
Effective length of query: 402
Effective length of database: 394
Effective search space:   158388
Effective search space used:   158388
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