GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araZsh in Pseudomonas simiae WCS417

Align Inner-membrane translocator (characterized, see rationale)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease

Query= uniprot:A0KWY7
         (320 letters)



>FitnessBrowser__WCS417:GFF2365
          Length = 325

 Score =  175 bits (444), Expect = 1e-48
 Identities = 104/295 (35%), Positives = 175/295 (59%), Gaps = 8/295 (2%)

Query: 15  LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74
           + + + +V  F  + F + R   ++LR  +   I A+GMT VI++ GIDLSVG+++A +G
Sbjct: 30  VFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAG 89

Query: 75  VVTSLLITEYQWHPLLAFVVI-LPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLAT 133
           + ++++ T  Q + LLA V   +  G + G + G ++    + PF+ TL  + +ARG+  
Sbjct: 90  LCSAMVAT--QGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTF 147

Query: 134 TLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRFGTNVYAI 193
            L++ S   D P     A +++ +   G + +  +IF +  +I  +V+ YT +G  VYA+
Sbjct: 148 ILNDGSPITDLPD----AYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAV 203

Query: 194 GGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAVV 253
           GGN+ SA   GI + K   S+Y +S  LA LAG+V +  T S      +  ELDAIAAVV
Sbjct: 204 GGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVV 263

Query: 254 IGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILL 308
           IGGT L+GG+G ++GT+ G +L+GVI   +   G +SS++ ++  GL++ F +L+
Sbjct: 264 IGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLG-VSSYYQQVAKGLIIVFAVLI 317


Lambda     K      H
   0.330    0.145    0.424 

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: 18
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: 320
Length of database: 325
Length adjustment: 28
Effective length of query: 292
Effective length of database: 297
Effective search space:    86724
Effective search space used:    86724
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: 48 (23.1 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