GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Dinoroseobacter shibae DFL-12

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)

Query= uniprot:A0A1N7UKA9
         (325 letters)



>FitnessBrowser__Dino:3606962
          Length = 357

 Score =  191 bits (486), Expect = 2e-53
 Identities = 115/313 (36%), Positives = 178/313 (56%), Gaps = 21/313 (6%)

Query: 27  LPLVFILLCVV---MAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGS 83
           +PL+ ++  +    +   S++F  +   + IL+Q  I GI+A   + VILT GIDLSVG+
Sbjct: 47  VPLIVLVAAIAVFGLLLGSKFFSPFALTL-ILQQVQIVGIVAAAQSLVILTAGIDLSVGA 105

Query: 84  ILAFAGLCSAMVATQGYGLLA--AVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSI 141
           I+  + +      T  YGL    AV+ G+  G +LG +NG++VA + +PPF+ TLGM  I
Sbjct: 106 IMVMSSVVMGQF-TFRYGLPVEVAVACGLLCGTLLGFINGWLVAKVKLPPFIVTLGMWQI 164

Query: 142 ARGMTFI-----------LNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMV 190
                F+           + D +P+       L +G  ++   GV  ++  V+ L +   
Sbjct: 165 VLAANFLYSRNETIRSQDIRDQAPLLQFFGTTLEIGGARL-TYGVIFMVLLVIVLAY--A 221

Query: 191 LRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQA 250
           LR+T +GR+VYAVG + ++A  SG+ V + + SVY++SGL+   AG  L  R  S  P +
Sbjct: 222 LRHTAWGRHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRIGSVSPTS 281

Query: 251 GVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLI 310
           G    +++I AVVIGG SL GG GSI+G  FGAL++GV   GL LLG  + +  +  GL+
Sbjct: 282 GQLANIESITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGADAQWTFLLIGLL 341

Query: 311 IVFAVLIDVWRKK 323
           I+ AV +D W +K
Sbjct: 342 IIAAVAVDQWIRK 354


Lambda     K      H
   0.326    0.141    0.412 

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: 245
Number of extensions: 7
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: 325
Length of database: 357
Length adjustment: 28
Effective length of query: 297
Effective length of database: 329
Effective search space:    97713
Effective search space used:    97713
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