GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galP in Bacteroides faecis MAJ27

Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_010537714.1 KCY_RS0114120 MFS transporter

Query= SwissProt::P0AEP1
         (464 letters)



>NCBI__GCF_000226135.1:WP_010537714.1
          Length = 309

 Score =  195 bits (496), Expect = 2e-54
 Identities = 108/306 (35%), Positives = 178/306 (58%), Gaps = 21/306 (6%)

Query: 11  NKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVGAV 70
           N +   F+  +AAL G LFG D  VI+G +  ++  FQ+ +  Q W V   + G+ VG +
Sbjct: 6   NFSYLIFLSVVAALGGFLFGYDTAVISGTIAQVSQLFQLDALQQGWYVGCALIGSIVGVL 65

Query: 71  GSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYL 130
            +G LS KLGRK +++I A+LF   +L  A + +   L++ R++ G+ +GV S  +PLY+
Sbjct: 66  FAGILSDKLGRKLTMVISAVLFSTSALGCAISADFTQLVIYRIIGGVGIGVVSIVSPLYI 125

Query: 131 SEIAPEKIRGSMISMYQLMITIGILGAYLSD------------------TAFSYTGAWRW 172
           SE++  + RG ++S+YQL +T+G LGAYL +                       T  WR 
Sbjct: 126 SEVSVAQYRGRLVSLYQLAVTVGFLGAYLVNYQLLGYAQSGSQLSIDWLNKIFVTEVWRG 185

Query: 173 MLGVIIIPAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESL 232
           MLG+ ++PA+L  I +FF+P+SPRW   K +   A  +L ++ ++ +EA  +L+E +  L
Sbjct: 186 MLGMEMLPAVLFFIIIFFIPESPRWLIVKGKEEKAVNILEKIYNSVSEATSQLNETKSVL 245

Query: 233 QVK-QSGWALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMW 291
             + +S WAL  +   F +AV +GV + ++ QF G+N ++YY P IFE AG +   + ++
Sbjct: 246 TSETKSEWALLMKPGIF-KAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSG-GDSLF 303

Query: 292 GTVIVG 297
             V+VG
Sbjct: 304 YQVLVG 309


Lambda     K      H
   0.327    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: 410
Number of extensions: 19
Number of successful extensions: 3
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: 464
Length of database: 309
Length adjustment: 30
Effective length of query: 434
Effective length of database: 279
Effective search space:   121086
Effective search space used:   121086
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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