GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Pedobacter sp. GW460-11-11-14-LB5

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate CA265_RS15045 CA265_RS15045 MFS transporter

Query= SwissProt::P11551
         (438 letters)



>FitnessBrowser__Pedo557:CA265_RS15045
          Length = 535

 Score =  105 bits (261), Expect = 5e-27
 Identities = 69/230 (30%), Positives = 104/230 (45%), Gaps = 22/230 (9%)

Query: 21  SRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIP 80
           +++Y      + ++FF W      N I +P  +  F LT F++ LI   FY GYFI  + 
Sbjct: 6   TKNYGTALYTIITVFFFWGFVAASNGIFIPFCKTHFKLTQFESQLIDFTFYGGYFIGSLI 65

Query: 81  AGI--------LMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLG 132
                      ++ K+ YK GII GL + A GA L  PA    ++   L   F+IA G  
Sbjct: 66  LYFASQASKVDILNKIGYKKGIIAGLIISAGGALLMIPAVHSGSFLFILFAFFVIALGFS 125

Query: 133 CLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKM 192
             +TAANPFV  LG   SG  RLNLA   N+FG ++  V    ++          V++  
Sbjct: 126 LQQTAANPFVVALGEPESGAHRLNLAGGINNFGGLMGPVIVSVVLFGTANDAVAKVVE-- 183

Query: 193 SPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDA 242
                       + S+   Y I+  + L VA+   ++K P + S    +A
Sbjct: 184 ------------ISSINNLYYILAGLFLGVAIFFGVSKLPDVTSTEKIEA 221



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 43/111 (38%), Positives = 62/111 (55%), Gaps = 1/111 (0%)

Query: 319 ISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQ 378
           I +  P K LA +  +     +I     GHV + A        SI +P+IFSL I  LG+
Sbjct: 403 IGQEKPAKTLAIFGTLGAIAMIIGLLTTGHVAIFAFVSGGLCCSIMWPSIFSLAITGLGK 462

Query: 379 DTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIFA 429
            T  GSSF++M I+GG I+ P+ G ++D+AG I  + +IP L FA +  FA
Sbjct: 463 YTSQGSSFLIMMILGGSIIPPIQGELADSAG-IHNSYIIPVLGFAYLIFFA 512


Lambda     K      H
   0.329    0.140    0.425 

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: 575
Number of extensions: 28
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 438
Length of database: 535
Length adjustment: 34
Effective length of query: 404
Effective length of database: 501
Effective search space:   202404
Effective search space used:   202404
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: 40 (21.8 bits)
S2: 52 (24.6 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