GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfB in Paraburkholderia bryophila 376MFSha3.1

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109) (characterized)
to candidate H281DRAFT_03366 H281DRAFT_03366 electron transfer flavoprotein beta subunit

Query= BRENDA::D2RIQ2
         (263 letters)



>FitnessBrowser__Burk376:H281DRAFT_03366
          Length = 249

 Score = 93.2 bits (230), Expect = 5e-24
 Identities = 68/216 (31%), Positives = 112/216 (51%), Gaps = 8/216 (3%)

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

Query: 59  ITMGPPHAESVLRDCLAVGADEAKLVSDRAFGGADTLATSAAMANTIKHFGVPDLILCGR 118
           ++ G   ++  LR  LA+GAD A L+          LA  A +   +     P L++ G+
Sbjct: 61  VSAGVTQSQETLRTALAIGADRAILIESSE--ELQPLAV-AKLLKALVDKEQPQLVILGK 117

Query: 119 QAIDGDTAQVGPEIAEHLGLPQVTAALKVQVKDDTVVVDRDNEQMSMTFTMKMPCVVTV- 177
           QAID D+ Q G  +A    LPQ T A KV V D    V R+ +  + T ++K+P VVT  
Sbjct: 118 QAIDDDSNQTGQMLAALANLPQATFASKVVVADGKATVSREVDGGAETLSLKLPAVVTTD 177

Query: 178 MRSKDLRFASIRGKMKARKAEIPVYTAAALEIPLDI 213
           +R  + R+ ++   MKA+K   P+ T    ++ +D+
Sbjct: 178 LRLNEPRYVTLPNIMKAKKK--PLETIRPEDLGVDV 211


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: 146
Number of extensions: 6
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: 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