GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Pseudomonas fluorescens GW456-L13

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)

Query= uniprot:A0A1N7UKA9
         (325 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122
          Length = 323

 Score =  201 bits (512), Expect = 2e-56
 Identities = 112/325 (34%), Positives = 182/325 (56%), Gaps = 3/325 (0%)

Query: 1   MNAKTITAPVTAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSI 60
           M  +  T P T  P + LR  LD + + L  + + V      + F++  N   +    S 
Sbjct: 2   MTTQNNTLPTTRKPLD-LRRFLDDWVMLLAAVGIFVACTLLIDNFLSPLNMRGLGLAIST 60

Query: 61  NGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVN 120
            GI A  M Y + +   DLSVGS++A AG+ +A+V      +   V A +  G ++G++N
Sbjct: 61  TGIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTNSVFLGVCAALVMGLIVGLIN 120

Query: 121 GFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIF 180
           G ++A L +   + TL  + I RG+ +I  +G  +    +++   G G++  + VPI+I 
Sbjct: 121 GIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILIT 180

Query: 181 AVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLS 240
            V  L F  +L YTTYGR   A+GGN+++A  +G+ V +    ++ V G++  LAGV+L+
Sbjct: 181 IVCFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILA 240

Query: 241 ARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSS 300
           +R TS  P  G  +EL  I+A V+GG SLSGG G I   + G L++ +I N +NL  + +
Sbjct: 241 SRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDT 300

Query: 301 YYQQVAKGLIIVFAVLIDVWRKKKR 325
           +YQ V +G I++ AV+ID  R K+R
Sbjct: 301 FYQYVIRGSILLLAVVID--RLKQR 323


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: 220
Number of extensions: 14
Number of successful extensions: 1
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: 323
Length adjustment: 28
Effective length of query: 297
Effective length of database: 295
Effective search space:    87615
Effective search space used:    87615
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