GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= uniprot:A0A1N7UKA9
         (325 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033
          Length = 325

 Score =  184 bits (467), Expect = 3e-51
 Identities = 112/301 (37%), Positives = 169/301 (56%), Gaps = 4/301 (1%)

Query: 27  LPLVFILLCVVMAFS--SEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSI 84
           L L   LL +V  FS  S +F+++  +  +  Q     +LAVGMT+V++  GIDLSVGS+
Sbjct: 21  LGLAGALLAMVALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSV 80

Query: 85  LAFAGLC-SAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIAR 143
           LA A    S  +   G+ +L A   GM   A+ G + G +     IP F+ +LG+L +AR
Sbjct: 81  LALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMAR 140

Query: 144 GMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAV 203
           G+ + +  GS    + DA+  L       I    II  ++  I   VL  T +GRY+  +
Sbjct: 141 GLAYQMT-GSRTAYIGDAFAWLSNPIAFGISPSFIIALLIIFIAQAVLTRTVFGRYLIGI 199

Query: 204 GGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVV 263
           G NE++ R +GI  +     V+ + GLLAG+A +   +R  +A P AG   EL  IAAVV
Sbjct: 200 GTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIAAVV 259

Query: 264 IGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRKK 323
           IGGTSL GG GS++ T FG L+I V+  GL  +G +   +++  G +IV AV++D +R +
Sbjct: 260 IGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQ 319

Query: 324 K 324
           +
Sbjct: 320 R 320


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: 236
Number of extensions: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 325
Length of database: 325
Length adjustment: 28
Effective length of query: 297
Effective length of database: 297
Effective search space:    88209
Effective search space used:    88209
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: 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