GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Tistlia consotensis USBA 355

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= uniprot:A0A1N7UKA9
         (325 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  215 bits (547), Expect = 1e-60
 Identities = 125/299 (41%), Positives = 180/299 (60%), Gaps = 4/299 (1%)

Query: 20  LSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDL 79
           L L   GL LV   +  V++  S YF+T  N  +IL Q+ + GIL++GMT+VILT GIDL
Sbjct: 32  LELRMLGLALV---IGAVLSLLSPYFLTESNIFNILDQSVVIGILSIGMTFVILTGGIDL 88

Query: 80  SVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGML 139
           SVGS+   +G+   + A + Y +  A+  G+  GA +G+V+G ++    +  FV TLGM+
Sbjct: 89  SVGSVAGLSGIVLGL-ALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLGMM 147

Query: 140 SIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRY 199
           +I R + +I +  + I+  P    ++    +  I   ++      L+ W  L YT  GR 
Sbjct: 148 AIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTKGGRT 207

Query: 200 VYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAI 259
           +YA+G N+++AR +G+GV       YVVSG LA +A     A+  S  P  G   ELDAI
Sbjct: 208 IYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDPLTGNGMELDAI 267

Query: 260 AAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLID 318
           AAVVIGG SL GG GSIVGTL G L++ +I NGLNLLGVS ++Q  A G II+ A+L++
Sbjct: 268 AAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMALLVE 326


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: 257
Number of extensions: 18
Number of successful extensions: 2
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: 335
Length adjustment: 28
Effective length of query: 297
Effective length of database: 307
Effective search space:    91179
Effective search space used:    91179
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 Apr 09 2024. 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