GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Cronobacter condimenti 1330

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate WP_007665341.1 BN137_RS16385 c-type cytochrome

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



>NCBI__GCF_000319285.1:WP_007665341.1
          Length = 398

 Score =  353 bits (905), Expect = e-102
 Identities = 203/418 (48%), Positives = 252/418 (60%), Gaps = 28/418 (6%)

Query: 1   MKALVIATLALLGSAAANAAEADQQALVQQGEYLARAGDCVACHTAKDGKPFAGGLPMET 60
           MK + +  LAL       A  A  QA+  +GEY+ARAGDC+ACHTA DG P AGG+   T
Sbjct: 1   MKRITVLALALW------ATHAGAQAM-SRGEYVARAGDCMACHTAADGAPLAGGVKFAT 53

Query: 61  PIGVIYSTNITPDKT-GIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQA 119
           P+G IYSTNITPD T GIG YS+EDF +A+R GVAK G  LYPAMP+PSYA++SD D++A
Sbjct: 54  PLGDIYSTNITPDNTHGIGGYSYEDFARAMREGVAKDGHHLYPAMPYPSYAKMSDEDLRA 113

Query: 120 LYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETP-APAAGSDPVISRGA 178
           LY Y M  V P A  N+DSDIPWPLSMRWPL IW  +FA   E P  P A      +RGA
Sbjct: 114 LYEYLMNEVKPQATANRDSDIPWPLSMRWPLGIWNSLFAD--EKPFTPRADKSAQWNRGA 171

Query: 179 YLVEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGSWS 238
           YLV+G GHCGACHTPR + MQEKA        FL+G   L GW A SLRG         S
Sbjct: 172 YLVQGPGHCGACHTPRGIGMQEKAFD-ERDEQFLAGE-ELNGWYAPSLRG------LKMS 223

Query: 239 EEQLVQFLKTGRSDRSAVFGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKDQPHQY 298
           E  L   L+ GRS  +A+ G M +VV +S QY++D D  AIA YL SLP ++P      +
Sbjct: 224 EGDLTLLLRDGRSKHAALSGPMDEVVTNSTQYLSDDDNRAIASYLLSLPGSEPVKTQAPH 283

Query: 299 DKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSADATSLIHI 358
             Q   AL NG        +Y   CA CH ++G G     PAL  N  + + +  +L+ +
Sbjct: 284 LSQA--ALENGHQ------LYARYCATCHASNGEGADYAVPALKDNLTVNADNPLTLLRV 335

Query: 359 VLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGDVAALR 416
           VL+GG    T      ++MP + W LSDQ+ ADV N+IR S+GN A+ V P  V   R
Sbjct: 336 VLEGGKTAVT-ERHLPYSMPGYGWALSDQDAADVTNYIRGSFGNHAAPVTPDQVKDAR 392


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: 627
Number of extensions: 45
Number of successful extensions: 8
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: 398
Length adjustment: 31
Effective length of query: 403
Effective length of database: 367
Effective search space:   147901
Effective search space used:   147901
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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