GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bamI in Marinobacter adhaerens HP15

Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate GFF4234 HP15_4174 formate dehydrogenase, alpha subunit

Query= uniprot:Q39TW6
         (218 letters)



>FitnessBrowser__Marino:GFF4234
          Length = 966

 Score =  109 bits (272), Expect = 2e-28
 Identities = 74/236 (31%), Positives = 108/236 (45%), Gaps = 34/236 (14%)

Query: 4   INLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVE-VRGWPKL 62
           ++L IDG ++   EG ++L AA   GI+IP LC  + LE +G CR+C VE+E  RG+P  
Sbjct: 29  VSLSIDGTDIAVPEGTSVLRAATLAGINIPKLCASDNLEAFGSCRMCAVEIEGRRGYP-- 86

Query: 63  VAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYGA 113
            A C  PV +G+ V T+N K+ K+R+ ++E  ++  P          + EL+ +A   G 
Sbjct: 87  -ASCTTPVSEGMTVTTQNAKLAKLRRNIMELYISDHPLDCLTCPANGNCELQDVAGAVGL 145

Query: 114 DRDRF----EKH---------------PSFCIHCGLCVRYCAEIKKKNAVGFVDRGSNRE 154
              R+    E H               PS CI C  C+R C E++   A+    RG + +
Sbjct: 146 REVRYGFEGENHLDVEVDDSNPYFSFDPSKCIVCSRCIRACEEVQGTFALTIDGRGFDSK 205

Query: 155 ISF--IPEIAAKECWDCKECFPLCPTSALQAAYVLAGALMTPPEEAHSGGCGCSCS 208
           +S          EC  C  C   CPTS L    V+               CG  CS
Sbjct: 206 VSAGQNDPFMDSECVSCGACVQACPTSTLMEKSVIDAGQPEHSVVTTCAYCGVGCS 261


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: 485
Number of extensions: 22
Number of successful extensions: 5
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: 966
Length adjustment: 33
Effective length of query: 185
Effective length of database: 933
Effective search space:   172605
Effective search space used:   172605
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: 51 (24.3 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