GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfB in Pseudomonas fluorescens FW300-N2C3

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109) (characterized)
to candidate AO356_20320 AO356_20320 electron transporter RnfB

Query= BRENDA::D2RIQ2
         (263 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20320
          Length = 249

 Score =  107 bits (267), Expect = 2e-28
 Identities = 75/215 (34%), Positives = 121/215 (56%), Gaps = 12/215 (5%)

Query: 1   MNIVVCVKQVPD-TAEMKIDPVTNNLVRDGVTNIMNPYDQYALETALQLKDE-LGAHVTV 58
           M ++V VK+V D   ++++    + +    V   MNP+ + A+E A++LK++ +   + V
Sbjct: 1   MKVLVAVKRVVDYNVKVRVKADNSGVDLANVKMSMNPFCEIAVEEAVRLKEKGVATEIVV 60

Query: 59  ITMGPPHAESVLRDCLAVGADEAKLVSDRAFGGADTLATSAAMANTIKHF---GVPDLIL 115
           +++GP  A+  LR  LA+GAD A LV       A+ L TS A+A  +K       P L++
Sbjct: 61  VSIGPTTAQEQLRTALALGADRAILVES-----AEDL-TSLAVAKLLKAVVDKEQPSLVI 114

Query: 116 CGRQAIDGDTAQVGPEIAEHLGLPQVTAALKVQVKDDTVVVDRDNEQMSMTFTMKMPCVV 175
            G+QAID D  Q G  +A   G  Q T A KV+V  D+V V R+ +  + T ++K+P +V
Sbjct: 115 LGKQAIDSDNNQTGQMLAALSGYGQGTFASKVEVSGDSVAVTREIDGGAQTVSLKLPAIV 174

Query: 176 TV-MRSKDLRFASIRGKMKARKAEIPVYTAAALEI 209
           T  +R  + R+AS+   MKA+K  + V T  AL +
Sbjct: 175 TTDLRLNEPRYASLPNIMKAKKKPLEVLTPDALGV 209


Lambda     K      H
   0.318    0.133    0.375 

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: 125
Number of extensions: 8
Number of successful extensions: 4
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: 263
Length of database: 249
Length adjustment: 24
Effective length of query: 239
Effective length of database: 225
Effective search space:    53775
Effective search space used:    53775
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 (21.7 bits)
S2: 47 (22.7 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