GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Streptacidiphilus oryzae TH49

Align 3-methyl-2-oxobutanoate dehydrogenase subunit beta; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit beta; BCKADH E1-beta; EC 1.2.4.4 (characterized)
to candidate WP_084704192.1 BS73_RS19370 alpha-ketoacid dehydrogenase subunit beta

Query= SwissProt::P9WIS1
         (348 letters)



>NCBI__GCF_000744815.1:WP_084704192.1
          Length = 373

 Score =  341 bits (874), Expect = 2e-98
 Identities = 173/320 (54%), Positives = 218/320 (68%), Gaps = 3/320 (0%)

Query: 27  TMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAII 86
           TM QA+NRAL DA+ AD  V + GEDV   GGVFRVT+GL   FG DRC DTPLAE+ I+
Sbjct: 38  TMAQALNRALRDALRADPSVHLLGEDVGALGGVFRVTDGLTAEFGEDRCTDTPLAEAGIV 97

Query: 87  GIAVGLALRGFVPVPEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFGGIG 146
           G AVG+A+ G  PV E+QFD F+YPAF+Q+ SH+AK R RT G + +P+TVRIP  GGIG
Sbjct: 98  GTAVGMAMYGLRPVVELQFDAFAYPAFEQLASHVAKMRNRTAGRLPLPLTVRIPYGGGIG 157

Query: 147 AAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYHGRGMVD 206
             EHH DS+E+Y+VHT GL V+ P+T  DAY +LR AIA  DPV++LEPKR Y  +   D
Sbjct: 158 GVEHHGDSSEAYYVHTPGLHVMAPATVEDAYGMLRAAIASDDPVVFLEPKRLYWSKAEWD 217

Query: 207 TSRP--EPPIGHAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVIDLRSLAPL 264
              P    P G A++RR G    ++ YG  V   L +A+ A +   W L V+DLRSL P 
Sbjct: 218 PEAPAATAPPGRAVLRREGRSAVLIAYGPSVPVCLEAAEAA-RADGWDLAVLDLRSLVPF 276

Query: 265 DFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQEEMFYQLEAPVLRACGFDTPYPPA 324
           D +T+ A+++RTGR VV+HE     G GA +AAR+ E  F+ LEAPVLR  GFD PYPP 
Sbjct: 277 DDETVCAAVRRTGRAVVVHESSGFAGVGAEIAARVTERCFHHLEAPVLRVAGFDIPYPPP 336

Query: 325 RLEKLWLPGPDRLLDCVERV 344
            LE+  LPG DR+LD V R+
Sbjct: 337 MLERHHLPGVDRILDAVARL 356


Lambda     K      H
   0.321    0.137    0.417 

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: 457
Number of extensions: 25
Number of successful extensions: 3
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: 348
Length of database: 373
Length adjustment: 29
Effective length of query: 319
Effective length of database: 344
Effective search space:   109736
Effective search space used:   109736
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 (21.9 bits)
S2: 49 (23.5 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