GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etfA in Acidovorax sp. GW101-3H11

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Ac3H11_3189 Electron transfer flavoprotein, alpha subunit

Query= BRENDA::Q18AQ5
         (336 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3189 Electron transfer
           flavoprotein, alpha subunit
          Length = 310

 Score =  153 bits (387), Expect = 5e-42
 Identities = 116/323 (35%), Positives = 164/323 (50%), Gaps = 15/323 (4%)

Query: 3   NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVI 62
           +VLV+ E     I+  +L  +  A     D    V+    G+            G  +VI
Sbjct: 2   SVLVIAEHDNASIKGATLNTVTAAVACGGDVHVLVAGHNAGAAAAAAGQIA---GVSKVI 58

Query: 63  VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122
             D   LA    E    AA     A +   +LF AT+ G+++APRV+A++     +D T 
Sbjct: 59  HADAAGLAHGLAE--NVAAQVLAIAGNYSHILFPATASGKNIAPRVAAKLDVAQISDITK 116

Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKV 182
           + V+ DT      RP + GN +AT+   D   ++ TVR              AV      
Sbjct: 117 V-VSADT----FERPIYAGNAIATVQSAD-AVKVVTVRTTGFDAAAATGGSAAVETAAAT 170

Query: 183 EFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLD-ILYELAEIIGGEVSG 241
              DA K   +   I +  +  ++  AKI+VS GR +G KE  D ++  LA+ +G  +  
Sbjct: 171 A--DAGKSSYLGSEIAKNDRP-ELTAAKIIVSGGRALGSKEKFDEVITPLADKLGAAIGA 227

Query: 242 SRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPI 301
           SRA +DAG+     QVGQTGK V P LYIA GISGAIQH+AGM+D++ IVAINK+PEAPI
Sbjct: 228 SRAAVDAGYAPNDLQVGQTGKIVAPQLYIAAGISGAIQHLAGMKDSKVIVAINKDPEAPI 287

Query: 302 FKYADVGIVGDVHKVLPELISQL 324
           F  AD G+  D+   +PEL+  L
Sbjct: 288 FSVADYGLEADLFTAVPELVKAL 310


Lambda     K      H
   0.316    0.135    0.371 

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: 261
Number of extensions: 18
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: 336
Length of database: 310
Length adjustment: 28
Effective length of query: 308
Effective length of database: 282
Effective search space:    86856
Effective search space used:    86856
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: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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