GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamI in Dechlorosoma suillum PS

Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate Dsui_3029 Dsui_3029 NADH:ubiquinone oxidoreductase chain G-like protein

Query= uniprot:Q39TW6
         (218 letters)



>FitnessBrowser__PS:Dsui_3029
          Length = 237

 Score = 79.7 bits (195), Expect = 4e-20
 Identities = 53/173 (30%), Positives = 79/173 (45%), Gaps = 29/173 (16%)

Query: 8   IDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVEVRGWPKLVAGCI 67
           +DGK VV  +G TIL+AA+  G  IP LC H     +G C++C V+V  R     V+ C 
Sbjct: 9   LDGKPVVFQDGQTILEAARQAGHYIPHLCWHPDFPAHGSCKLCIVKVGGRH----VSSCA 64

Query: 68  YPVEKGLVVRTRNEKIDKIRKVLLE-------------------EMLAHAPDSEELKALA 108
            P ++G+ V +   +++  R+ LL+                   ++ A A D E L A  
Sbjct: 65  MPAKEGMEVESNTPEMNGERRALLQMLFVEGNHFCPSCEKSGNCQLQALAYDLEMLSAHF 124

Query: 109 QEYGADRDRFEKHPSF------CIHCGLCVRYCAEIKKKNAVGFVDRGSNREI 155
             +  +R     HP        CI C LCVR   +I  KN     DRG ++ +
Sbjct: 125 NHFYPNRPVDASHPDVLLDFNRCIFCELCVRASRDIDGKNIFALTDRGIHKHL 177


Lambda     K      H
   0.320    0.137    0.432 

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: 150
Number of extensions: 7
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: 218
Length of database: 237
Length adjustment: 22
Effective length of query: 196
Effective length of database: 215
Effective search space:    42140
Effective search space used:    42140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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