GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Pseudomonas simiae WCS417

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= uniprot:B2T9V8
         (351 letters)



>FitnessBrowser__WCS417:GFF2365
          Length = 325

 Score =  166 bits (421), Expect = 6e-46
 Identities = 104/323 (32%), Positives = 173/323 (53%), Gaps = 13/323 (4%)

Query: 21  LALPASRGKRARSELARLRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALV 80
           +  P +   R R  L+ L    L     LL V+ AF S  F+T  N + +L  ++   ++
Sbjct: 6   ITAPVTAAPRNRLRLS-LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGIL 64

Query: 81  VLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVI 140
            +  + ++LT   DLS+ S +  A    AM+    A+ G+G+    +AG+ A    GA++
Sbjct: 65  AVGMTYVILTKGIDLSVGSILAFAGLCSAMV----ATQGYGLLAAVSAGMFA----GAML 116

Query: 141 GFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIV--LGLP 198
           G +NGF+V  L +  F+ TL ML + RGM      G  + D+P ++ AL    +  +G+P
Sbjct: 117 GVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVP 176

Query: 199 LSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASV 258
           + ++   A   I   +LRY   GR +YA+GGN ++AR +GI V ++ + V+V+  +LA +
Sbjct: 177 IIIFAVVAL--IFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGL 234

Query: 259 GGLIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLT 318
            G++++    +     G        AA VIGG SL GG G++ G L G LL+GV+ N L 
Sbjct: 235 AGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLN 294

Query: 319 LAQVPSFWIQAIYGAIILGSLMV 341
           L  V S++ Q   G II+ ++++
Sbjct: 295 LLGVSSYYQQVAKGLIIVFAVLI 317


Lambda     K      H
   0.326    0.140    0.397 

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: 246
Number of extensions: 12
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: 351
Length of database: 325
Length adjustment: 28
Effective length of query: 323
Effective length of database: 297
Effective search space:    95931
Effective search space used:    95931
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 (21.6 bits)
S2: 49 (23.5 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