GapMind for catabolism of small carbon sources

 

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

Align 3-methyl-2-oxobutanoate dehydrogenase subunit alpha; Branched-chain alpha-ketoacid dehydrogenase E1 component subunit alpha; BCKADH E1-alpha; EC 1.2.4.4 (characterized)
to candidate WP_050655238.1 C1M55_RS19770 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha

Query= SwissProt::P9WIS3
         (367 letters)



>NCBI__GCF_002893965.1:WP_050655238.1
          Length = 362

 Score =  290 bits (743), Expect = 3e-83
 Identities = 160/348 (45%), Positives = 207/348 (59%), Gaps = 4/348 (1%)

Query: 19  PVQLVGPDGTPTAERRYHR---DLPEETLRWLYEMMVVTRELDTEFVNLQRQGELALYTP 75
           PVQL+ P+G       + R   D+  + L  LY  +VV+R +DTE V LQRQGE+ L+ P
Sbjct: 8   PVQLIQPNGARVCRPEFDRLITDIGPDELLSLYRDLVVSRRIDTEAVALQRQGEIGLWAP 67

Query: 76  CRGQEAAQVGAAACLRKTDWLFPQYRELGVYLVRGIPPGHVGVAWRGTWHGGLQFTTKCC 135
             GQEAAQVG+A  L   D+ F  YRE  V   RG+PP  +   WRG  H G        
Sbjct: 68  MLGQEAAQVGSARALAPGDFAFTSYREHAVAYCRGVPPELLTTMWRGISHSGWDPEQFSV 127

Query: 136 APMSVPIGTQTLHAVGAAMAAQRLDEDSVTVAFLGDGATSEGDVHEALNFAAVFTTPCVF 195
              ++ +G+Q LHA G A+ A     +  T+A+ GDGATS+GD+ EA+ FAA F    VF
Sbjct: 128 TNPAIVVGSQGLHATGYALGAHLDGAEIATIAYFGDGATSQGDIAEAMGFAASFRVGVVF 187

Query: 196 YVQNNQWAISMPVSRQTAAPSIAHKAIGYGMPGIRVDGNDVLACYAVMAEAAARARAGDG 255
           + QNNQWAIS PVS Q+  P I+H+AIGYG+P IRVDGNDVLA  AV   A  RAR G G
Sbjct: 188 FCQNNQWAISEPVSLQSRTP-ISHRAIGYGIPAIRVDGNDVLAVLAVTRSALNRAREGSG 246

Query: 256 PTLIEAVTYRLGPHTTADDPTRYRSQEEVDRWATLDPIPRYRTYLQDQGLWSQRLEEQVT 315
           PT IEA+T R+GPHTT+DDP+RYR+  ++  W + DP+ R R  L  + L  +     + 
Sbjct: 247 PTFIEAITCRMGPHTTSDDPSRYRTDTDMSEWRSRDPLERMRLLLGRRDLLGENELSTIA 306

Query: 316 ARAKHVRSELRDAVFDAPDFDVDEVFTTVYAEITPGLQAQREQLRAEL 363
           A A  V + LR A     D     +F  VYAE  P + A+RE+ RA L
Sbjct: 307 AAADDVAAGLRRATIALADPPPSALFDHVYAEAHPLIDAEREEHRAHL 354


Lambda     K      H
   0.320    0.134    0.413 

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: 371
Number of extensions: 15
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: 367
Length of database: 362
Length adjustment: 29
Effective length of query: 338
Effective length of database: 333
Effective search space:   112554
Effective search space used:   112554
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: 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