GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Pseudomonas simiae WCS417

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__WCS417:GFF2365
          Length = 325

 Score =  244 bits (623), Expect = 2e-69
 Identities = 144/314 (45%), Positives = 207/314 (65%), Gaps = 16/314 (5%)

Query: 29  LHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVIL 88
           L R G+  V ++L ++    + Y        F +  N M+ILRQ +IN +LA GMT+VIL
Sbjct: 22  LDRFGLPLVFILLCVVMAFSSEY--------FMTWRNWMDILRQTSINGILAVGMTYVIL 73

Query: 89  TAGIDLSVGSVLAVSAVLGMQVSL-GAAPGWAIPMFIFSGLVMGMVNGAMVALLNINAFV 147
           T GIDLSVGS+LA + +    V+  G     A+   +F+G ++G+VNG MVA L+I  FV
Sbjct: 74  TKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFV 133

Query: 148 VTLGTMTAFRGAAYLLADGTTVLNNDIP-SFEWIGNGDF--LHVPWLIWVAVAVVLLSWV 204
            TLG ++  RG  ++L DG+ +   D+P ++  +G G    + VP +I+  VA++   W+
Sbjct: 134 ATLGMLSIARGMTFILNDGSPI--TDLPDAYLALGIGKIGPIGVPIIIFAVVALIF--WM 189

Query: 205 ILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGN 264
           +LR T  G ++YA+GGN ++AR +GI V  V+  VY +SGL +GLAG + ++R   A   
Sbjct: 190 VLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQ 249

Query: 265 WGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGA 324
            G  YELDAIAAVV+GGTSL GG GSI GT+ GAL+IGV+NNGL +LG+SS++Q VAKG 
Sbjct: 250 AGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGL 309

Query: 325 VIVLAVILDKWRQK 338
           +IV AV++D WR+K
Sbjct: 310 IIVFAVLIDVWRKK 323


Lambda     K      H
   0.324    0.138    0.417 

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: 338
Number of extensions: 14
Number of successful extensions: 4
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: 344
Length of database: 325
Length adjustment: 28
Effective length of query: 316
Effective length of database: 297
Effective search space:    93852
Effective search space used:    93852
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 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