GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfA in Pseudomonas fluorescens FW300-N1B4

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Pf1N1B4_5613 Electron transfer flavoprotein, alpha subunit

Query= BRENDA::Q18AQ5
         (336 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5613
          Length = 318

 Score =  153 bits (387), Expect = 5e-42
 Identities = 109/313 (34%), Positives = 162/313 (51%), Gaps = 14/313 (4%)

Query: 10  QRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVIVVDDEAL 69
           Q   V+   +L  +  A +I  D    V+   +GS  E         G  +V+V D+ A 
Sbjct: 14  QDNKVLAPATLNTVAAAAKIGGDIHVLVAGAFVGSVAEAAAKIA---GVAKVLVADNAAY 70

Query: 70  AVYTTEPYTKAAYEAIKAADPIV--VLFGATSIGRDLAPRVSARIHTGLTADCTGLAVAE 127
           A    E         +     I   VL  ATS G+++ PRV+A++     ++   +  A+
Sbjct: 71  AYQLPENVAPLVAGLVIEQRTIYSHVLASATSNGKNILPRVAAQLDADQISEIISVESAD 130

Query: 128 DTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKVEFNDA 187
             K     RP + GN +AT+   +   ++ TVR         +    AV        +DA
Sbjct: 131 TFK-----RPIYAGNAIATVQ-SNAAVKVITVRATGFDPVAAEGGSAAV--EAVAAAHDA 182

Query: 188 DKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGSRATID 247
                V + + ++ +  ++  AKI+VS GRGM   +N   LY LA+ +G  V  SRA +D
Sbjct: 183 GISTFVGEELAKSDRP-ELTAAKIVVSGGRGMQNGDNFKHLYALADKLGAAVGASRAAVD 241

Query: 248 AGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIFKYADV 307
           AG++    QVGQTGK V P LYIA GISGAIQH+AGM+D++ IVAINK+ EAPIF+ AD 
Sbjct: 242 AGFVPNDMQVGQTGKIVAPQLYIAVGISGAIQHLAGMKDSKVIVAINKDEEAPIFQVADY 301

Query: 308 GIVGDVHKVLPEL 320
           G+V D+ + +PE+
Sbjct: 302 GLVADLFEAIPEM 314


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: 272
Number of extensions: 9
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: 318
Length adjustment: 28
Effective length of query: 308
Effective length of database: 290
Effective search space:    89320
Effective search space used:    89320
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.

Links

Downloads

Related tools

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