GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yjcH in Dinoroseobacter shibae DFL-12

Align small component of D-alanine uptake system, with Psest_0347 (actP-like) (characterized)
to candidate 3610174 Dshi_3555 hypothetical protein (RefSeq)

Query= reanno::psRCH2:GFF345
         (87 letters)



>FitnessBrowser__Dino:3610174
          Length = 85

 Score =  146 bits (368), Expect = 5e-41
 Identities = 65/87 (74%), Positives = 76/87 (87%), Gaps = 2/87 (2%)

Query: 1  MADNDKENAAAYWKANVRLITWSLVVWALVSYGFGILLRPLVAGIPVGGTDLGFWFAQQG 60
          MADN   NA  YW AN+R+ITW LV+WA+ SYGF ILLRPL++GIP+GGTDLGFWFAQQG
Sbjct: 1  MADNSSTNA--YWAANIRIITWCLVIWAVASYGFAILLRPLLSGIPIGGTDLGFWFAQQG 58

Query: 61 SIITFIAIIFHYAWRLNKLDKEFGVEE 87
          SI+ F+A+IF YAWR+NKLDKEFGVEE
Sbjct: 59 SILVFLALIFFYAWRMNKLDKEFGVEE 85


Lambda     K      H
   0.326    0.142    0.469 

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: 90
Number of extensions: 2
Number of successful extensions: 1
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: 87
Length of database: 85
Length adjustment: 9
Effective length of query: 78
Effective length of database: 76
Effective search space:     5928
Effective search space used:     5928
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 38 (20.7 bits)
S2: 38 (19.2 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