GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate Echvi_0200 Echvi_0200 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit

Query= metacyc::MONOMER-11684
         (327 letters)



>FitnessBrowser__Cola:Echvi_0200
          Length = 804

 Score =  174 bits (442), Expect = 5e-48
 Identities = 103/297 (34%), Positives = 162/297 (54%), Gaps = 7/297 (2%)

Query: 8   DAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVG 67
           + +     + +  D RVF  GEDVG+ G V +A AGL E+ GE RV DT + E  I G G
Sbjct: 475 EVLQACFDQMLSNDPRVFAFGEDVGKIGDVNQAFAGLQEKHGELRVTDTGIREMTIIGQG 534

Query: 68  IGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGAL 127
           IG A+ G+RPIAE+Q+ D+I  A+  +  + A + YR+      P++VR   G  + G  
Sbjct: 535 IGTALRGLRPIAEIQYLDYIYYALMTLTDDLACLHYRTKGGQKAPMIVRT-RGHRLEGVW 593

Query: 128 YHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLIKGEVPAD 187
           +    + AI  +  GL + +P     A G+    +R ++P L  E   AYR  K  +P +
Sbjct: 594 HSGSPMSAILGSLRGLLVCVPRNMTQAAGMYNTLLRSDEPALMIECLNAYRQ-KELMPTN 652

Query: 188 --DYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDKE 245
             ++ +P+G+ +V REG DITV+TYG      L AAE+L + G+S  V+D++T+ P D +
Sbjct: 653 VGEFTVPLGRPEVLREGTDITVVTYGAMCRIVLDAAEQLVEYGVSVEVIDVQTLLPFDVD 712

Query: 246 -AIIEAASKTGKVLLVTEDTKEGSIMSEVAAII-SEHCLFDLDA-PIKRLAGPDIPA 299
             I+E+  KT +V+   ED   G+    +  ++  +   + LD+ P+   A P  PA
Sbjct: 713 HVILESIKKTSRVIFADEDVPGGASAYMMQQVLEKQKAYYQLDSEPVTLSAQPHRPA 769


Lambda     K      H
   0.319    0.136    0.392 

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: 559
Number of extensions: 29
Number of successful extensions: 4
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: 327
Length of database: 804
Length adjustment: 34
Effective length of query: 293
Effective length of database: 770
Effective search space:   225610
Effective search space used:   225610
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: 52 (24.6 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