GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfA in Pseudomonas fluorescens FW300-N2E2

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Pf6N2E2_5984 Electron transfer flavoprotein, alpha subunit

Query= BRENDA::Q18AQ5
         (336 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5984
          Length = 309

 Score =  150 bits (380), Expect = 3e-41
 Identities = 109/320 (34%), Positives = 157/320 (49%), Gaps = 20/320 (6%)

Query: 4   VLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVIV 63
           +LV+ E     +   +L  +  A +I  D    V+    G+  E         G  +V+ 
Sbjct: 3   ILVIAEHDNKALAPATLNTVAAAAKIGGDIHVLVAGQGAGAVAEAAAKIA---GVAKVLS 59

Query: 64  VDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTGL 123
            D+ A A    E       E  K    I  L  ATS G+++ PRV+A +     ++   +
Sbjct: 60  ADNAAYAHQLPENVAPLVAELGKGYSHI--LAAATSNGKNILPRVAAALDVDQISEIISV 117

Query: 124 AVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKVE 183
             A+  K     RP + GN +AT+       Q S     +  +    +   A      VE
Sbjct: 118 ESADTFK-----RPIYAGNAIATV-------QSSAAVKVITVRATGFDPVAAEGGSAAVE 165

Query: 184 FNDADKLVQVVQVIKEA---KKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVS 240
              A     +   + E      + ++  AKI+VS GRGM   +N   LY LA+ +G  V 
Sbjct: 166 ALGAAHDAGISSFVNEELAKSDRPELTAAKIVVSGGRGMQNGDNFKHLYALADKLGAAVG 225

Query: 241 GSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAP 300
            SRA +DAG++    QVGQTGK V P LYIA GISGAIQH+AGM+D++ IVAINK+ EAP
Sbjct: 226 ASRAAVDAGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDEEAP 285

Query: 301 IFKYADVGIVGDVHKVLPEL 320
           IF+ AD G+V D+ + +PEL
Sbjct: 286 IFQVADYGLVADLFEAIPEL 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: 259
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
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