GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Rhodococcus qingshengii djl-6-2

Align 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_050656427.1 C1M55_RS25425 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha

Query= SwissProt::P12694
         (445 letters)



>NCBI__GCF_002893965.1:WP_050656427.1
          Length = 327

 Score =  131 bits (329), Expect = 4e-35
 Identities = 95/301 (31%), Positives = 143/301 (47%), Gaps = 15/301 (4%)

Query: 116 DRILYESQRQGRISFYMTNYGEEGTHVGSAAALDNTDLVFGQYREAGVLMYRDYPLELFM 175
           D +    +  G   F+    G+EG   G+ AA+ + D +F Q R A   + +   +   +
Sbjct: 38  DAVQIHIRDHGFAGFWHPGKGQEGAVAGAVAAMRDDDYLFYQGRGATWPLAKGMTMGPII 97

Query: 176 AQCYGNI--SDLGKGRQMPVHYGCKERHFVTISSPLATQIPQAVGAAYAAKRANANRVVI 233
               G +  S  GKG  +P H+       +   + L +  P A GAA +A+     +V +
Sbjct: 98  GDLLGKVTGSTGGKGAGVP-HWADPALGIMGEGATLGSVYPVAAGAALSAQMRGTGQVAL 156

Query: 234 CYFGEGAASEGDAHAGFNFAATLECPIIFFCRNNGYAISTPTSEQYRGDGIAARGPGYGI 293
             FG+G A+ G  H     A+  + P+++FC NNG +++TP         IA R   YGI
Sbjct: 157 ADFGDGTAARGTFHETLLEASRWKLPLVYFCENNGISVTTPFESVSPTRTIAERATAYGI 216

Query: 294 MSIRVDGNDVFAVYNATKEARRRAVAENQPFLIEAMTYRIGHHSTSDDSSAYRSVDEVN- 352
             +RVDG+D  AVY+ATK A  RA     P LIEA+  R+G H    D+  YR  D ++ 
Sbjct: 217 PGVRVDGHDAVAVYHATKAAIDRARDGQGPSLIEAVVTRVGGH-WEGDAQKYRPEDFLST 275

Query: 353 YWDKQDHPISRLRHYLLSQGWWDEEQEKAWRKQSRRKVMEAFEQAERKPKPNPNLLFSDV 412
           Y D  D   SRL   L  Q              +R +V EA  +AE  P P+P+++  DV
Sbjct: 276 YRDPLDIMRSRLDALLADQ----------IVAAARAEVAEALAEAEAAPLPDPSVIMKDV 325

Query: 413 Y 413
           +
Sbjct: 326 F 326


Lambda     K      H
   0.320    0.135    0.405 

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: 353
Number of extensions: 20
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: 445
Length of database: 327
Length adjustment: 30
Effective length of query: 415
Effective length of database: 297
Effective search space:   123255
Effective search space used:   123255
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: 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