GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctB in Pseudomonas stutzeri RCH2

Align TctB aka STM2787, component of The tricarboxylate transporter, TctABC (characterized)
to candidate GFF206 Psest_0207 hypothetical protein

Query= TCDB::Q9FA45
         (144 letters)



>FitnessBrowser__psRCH2:GFF206
          Length = 147

 Score =  110 bits (275), Expect = 9e-30
 Identities = 60/137 (43%), Positives = 86/137 (62%), Gaps = 1/137 (0%)

Query: 5   RIFAGIWLLLCIAGLFIAWQIQSEYSYEPVGPRPFPLGIIGLMALCALALLLR-HPDTVS 63
           R+FA +WLL C     +AW  ++ ++Y+PVGPR +PL ++ LM   AL LL++ H +   
Sbjct: 4   RVFAAVWLLACAGLALLAWGFEAPFAYDPVGPRAYPLLLLFLMFCGALWLLIKPHGEPTP 63

Query: 64  WPRRHVLQKLITMIIILLMYAWGFEWLGFPIATALLTMVIGMLFGATIPAAGISGAVLGI 123
              R   Q+ +  ++ LL YA  FE LGF I+TAL    +G+LF   +  + ISGA+LG+
Sbjct: 64  AFDRAKAQRAVLCVLALLTYALLFEILGFVISTALAGFALGLLFNGRLWPSLISGALLGV 123

Query: 124 LLWYAFDRLLDVTLPLG 140
           LL+  FD LLDV LPLG
Sbjct: 124 LLYGLFDYLLDVPLPLG 140


Lambda     K      H
   0.332    0.147    0.498 

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: 122
Number of extensions: 11
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: 144
Length of database: 147
Length adjustment: 16
Effective length of query: 128
Effective length of database: 131
Effective search space:    16768
Effective search space used:    16768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 42 (20.8 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