GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacB' in Sphingomonas koreensis DSMZ 15582

Align lacB: cytochrome c2 component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate Ga0059261_0551 Ga0059261_0551 Cytochrome c2

Query= reanno::Caulo:CCNA_01704
         (120 letters)



>FitnessBrowser__Korea:Ga0059261_0551
          Length = 127

 Score = 92.8 bits (229), Expect = 1e-24
 Identities = 53/112 (47%), Positives = 72/112 (64%), Gaps = 4/112 (3%)

Query: 6   LTLAAVFAALASGAVAAPSGQQLFEQRCGMCHSLQQAPGK--MGPPLAGVVGRKAASFPG 63
           + LAA+ AALA  + A  SG       C  CH+  +  GK  +GP L G++G+ AA+ PG
Sbjct: 12  VALAALGAALAP-SFAQTSGAPAAFAACRACHTANKG-GKNGLGPNLYGIIGKPAAAVPG 69

Query: 64  YTYSAALKGSGITWTADKLDAYSKAPTKVVPGTKMLLGAPNDAERAAVIAYL 115
            +YSAALKGS + W    LDA+   P+K VPGT+M +G P+ A+RAA+IAYL
Sbjct: 70  VSYSAALKGSKLKWDEKTLDAFLANPSKKVPGTRMPIGTPDPAKRAAIIAYL 121


Lambda     K      H
   0.317    0.129    0.377 

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: 69
Number of extensions: 3
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: 120
Length of database: 127
Length adjustment: 14
Effective length of query: 106
Effective length of database: 113
Effective search space:    11978
Effective search space used:    11978
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: 41 (20.4 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