GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfA in Azospirillum brasilense Sp245

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate AZOBR_RS29735 AZOBR_RS29735 electron transfer flavoprotein subunit beta

Query= BRENDA::Q18AQ5
         (336 letters)



>FitnessBrowser__azobra:AZOBR_RS29735
          Length = 309

 Score =  165 bits (418), Expect = 1e-45
 Identities = 117/322 (36%), Positives = 173/322 (53%), Gaps = 22/322 (6%)

Query: 3   NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHY-GADEV 61
           ++LV+ E     ++  +L  +  A +I  D    +  L+ G   + + +  A   G  +V
Sbjct: 2   SILVIAEHDNAALKAATLNAVSAAAKIGGD----IHVLVAGQGAQAVAEAAATVAGVAKV 57

Query: 62  IVVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCT 121
           ++ DD A A    E          K      VL  A+S G++L PRV+A +     +D T
Sbjct: 58  LLADDAAYAHPLPENVAPLVVNLAKGYGH--VLAAASSEGKNLLPRVAALLDVAAISDIT 115

Query: 122 GLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEP---DETKEAVIN 178
           G+ V+ DT      RP + GN +AT+   D   ++ TVR    +         T E++  
Sbjct: 116 GV-VSADT----FERPIYAGNAIATVKSAD-PIKVVTVRTTAFEAAAATGGSATVESIAG 169

Query: 179 RFKVEFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGE 238
                  DA     V Q + ++++  ++  AKI+VS GRGM   EN  +L  LA+ +G  
Sbjct: 170 T-----GDAGSARFVGQELTKSERP-ELTQAKIVVSGGRGMQSGENFKLLEALADKLGAA 223

Query: 239 VSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPE 298
           V  SRA +DAG++    QVGQTGK V P+LYIA GISGAIQH+AGM+D++ IVAINK+ E
Sbjct: 224 VGASRAAVDAGFVPNDYQVGQTGKIVAPELYIAVGISGAIQHLAGMKDSKVIVAINKDEE 283

Query: 299 APIFKYADVGIVGDVHKVLPEL 320
           APIF+ AD G+V D+ K +PEL
Sbjct: 284 APIFQVADYGLVADLFKAVPEL 305


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: 273
Number of extensions: 12
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: 336
Length of database: 309
Length adjustment: 28
Effective length of query: 308
Effective length of database: 281
Effective search space:    86548
Effective search space used:    86548
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:

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