GapMind for catabolism of small carbon sources

 

Aligments 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_RS05475 AZOBR_RS05475 protein fixB

Query= BRENDA::Q18AQ5
         (336 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS05475 AZOBR_RS05475 protein fixB
          Length = 359

 Score =  263 bits (672), Expect = 5e-75
 Identities = 136/321 (42%), Positives = 204/321 (63%), Gaps = 4/321 (1%)

Query: 4   VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGS---KVEGLIDTLAHYGADE 60
           + V++EQ    + +VS EL+G+A ++A     +V A++LG+   ++  +      YGAD 
Sbjct: 24  IWVIVEQERGSVHSVSWELVGEARKLADKLGVEVGAVVLGADSPELNAICGDAFTYGADV 83

Query: 61  VIVVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADC 120
           V  V D  LA Y T+PYT+   + +    P +VL GAT++GRDLA  ++  + TGLTADC
Sbjct: 84  VYKVTDPVLADYRTDPYTRVMTDVVNTYKPEIVLLGATTLGRDLAGAIATTLATGLTADC 143

Query: 121 TGLAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRF 180
           T L +  D + L  TRP FGG ++ TI    +RPQM+TVRP VM   + D+++   +   
Sbjct: 144 TELDIYMDNRSLAATRPTFGGTLLCTIQTLAYRPQMATVRPRVMSMPDRDDSRTGRVVEV 203

Query: 181 KVEFNDADKLVQVVQVIKEAKK-QVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEV 239
                + D + +V+  I + ++ + ++  A I+V+AG+G+G  ENL ++++LA+++GGEV
Sbjct: 204 FPNLRETDVITKVLSFIADREQTEAQLAFADIIVAAGKGLGKPENLKLVFDLAKVLGGEV 263

Query: 240 SGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEA 299
             +R  + AGW    RQVGQTGKTVRP LYIA GISGAIQH  GME ++ I+AIN +P A
Sbjct: 264 GVTRPLVQAGWTGFDRQVGQTGKTVRPKLYIAAGISGAIQHRVGMEKSDLILAINTDPNA 323

Query: 300 PIFKYADVGIVGDVHKVLPEL 320
           PIF +A +G+VGD   +LP L
Sbjct: 324 PIFDFAHLGLVGDALTILPAL 344


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: 342
Number of extensions: 10
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: 359
Length adjustment: 29
Effective length of query: 307
Effective length of database: 330
Effective search space:   101310
Effective search space used:   101310
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: 49 (23.5 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