GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Pseudomonas fluorescens FW300-N2E2

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Pf6N2E2_1003 Fucose permease

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1003
          Length = 460

 Score =  255 bits (651), Expect = 2e-72
 Identities = 150/423 (35%), Positives = 231/423 (54%), Gaps = 23/423 (5%)

Query: 20  ERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMS 79
           E+ +   +A   +TS+FFMWG    L D+L  H +    ++  ++ LVQ  +FGAYF+++
Sbjct: 56  EKLSSTRLAFIFVTSLFFMWGLSHGLLDVLNKHFQDTLHISRGQSGLVQTAYFGAYFIIA 115

Query: 80  LPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAA 139
           LP GL + R GYK GI+AGLA+  +GA  F PA+ +  +  FL ALFVLA G+  L+ AA
Sbjct: 116 LPVGLFMERFGYKAGILAGLALFAIGALLFIPASMVGTFMPFLVALFVLACGLGCLETAA 175

Query: 140 NAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVA 199
           N Y A LG    +  RLT AQ+ N LG F+ P  GG +                 A  + 
Sbjct: 176 NLYAAALGDPAKSEQRLTFAQSFNGLGAFIGPVIGGAVFF---------------APPIE 220

Query: 200 YRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPAL-TEKTEQASVKQHSLVSPLRHPHVL 258
           +       V   Y  LAI++ L+ V     +LP +  EK+    +     VS  +  +  
Sbjct: 221 FNGNRVDLVSVTYAALAIIVMLMFVAFARIQLPEIRNEKSSDVLLPSAGEVSLWKKSNFT 280

Query: 259 FGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLA 318
             ++A F  VG  V IG+F +NY ++     +S Q A+  ++   L  M+GRF G+ ++ 
Sbjct: 281 GALVAQFCNVGAYVGIGAFFINY-AIDHWQGISAQKASYLLSLGMLAYMVGRFAGTWVMR 339

Query: 319 KLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMT 378
            +  R LL + + ++M L +  +     +++++V +I LF S+M+PTIF++GI  +G  T
Sbjct: 340 YVPARSLLILNSLVSMVLCIVAIAGFERISIFAVAAIYLFMSVMYPTIFAMGIRGLGTQT 399

Query: 379 GEASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSRIKSDTPV 438
            +A S L+M +VGGA VP + G  ADH G+  AF++PL C+A I +YGL      S  PV
Sbjct: 400 KKAGSCLVMTLVGGAFVPLLMGALADHFGIAAAFYVPLACFAAIAWYGL------SQPPV 453

Query: 439 AAT 441
            A+
Sbjct: 454 TAS 456


Lambda     K      H
   0.327    0.140    0.414 

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: 553
Number of extensions: 33
Number of successful extensions: 5
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: 442
Length of database: 460
Length adjustment: 33
Effective length of query: 409
Effective length of database: 427
Effective search space:   174643
Effective search space used:   174643
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 (21.7 bits)
S2: 51 (24.3 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