GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Dyella japonica UNC79MFTsu3.2

Align Glucose/galactose transporter (characterized, see rationale)
to candidate N515DRAFT_1918 N515DRAFT_1918 MFS transporter, FHS family, L-fucose permease

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1918
          Length = 442

 Score =  427 bits (1097), Expect = e-124
 Identities = 222/412 (53%), Positives = 294/412 (71%), Gaps = 12/412 (2%)

Query: 21  NYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVSIPAG 80
           +Y  A+  LTS+FFMWGF+TCLNDILIPHLKAVF LNY +AML+QF FFGAYFL+S+PAG
Sbjct: 24  DYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQFTFFGAYFLMSLPAG 83

Query: 81  QLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAANPYV 140
            LV RLGY+KGIV GL +A +G   F+PAA+   Y  FLGALFVLA+GIT+LQVAAN YV
Sbjct: 84  LLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVLATGITVLQVAANAYV 143

Query: 141 NALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQAN---------A 191
             LG  ++ASSRL L QA N+LGT +AP FG +LILS A   + ++A+ +          
Sbjct: 144 ALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAAVLSAEQIAKLSPAEQVAYRVQ 203

Query: 192 EAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLG 251
           EA+ V+ PYL LA  L +LA+      LP + E ++ A+  V+ H    S L+  H++ G
Sbjct: 204 EAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQAS--VKQH-SLVSPLRHPHVLFG 260

Query: 252 AVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVMQKI 311
            + IF YVG EV+IGSFLVN+L    I  M E+ AA+++AYYW GAM+GRFIGSA++ K+
Sbjct: 261 VLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAMIGRFIGSALLAKL 320

Query: 312 PAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPHTSQ 371
               +LA  A +   LVL  M T G+VAM++++ +GLFNSIMFPTIFSL +  +GP T +
Sbjct: 321 SPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMFPTIFSLGIERMGPMTGE 380

Query: 372 GSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKGSKM 423
            S +L +AIVGGAIVP +QG+ AD++G+Q AF LP++CY +I+FYG  GS++
Sbjct: 381 ASSLLIMAIVGGAIVPFVQGLFADHIGVQHAFFLPLLCYAYIVFYGLYGSRI 432


Lambda     K      H
   0.326    0.138    0.402 

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: 576
Number of extensions: 25
Number of successful extensions: 4
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: 423
Length of database: 442
Length adjustment: 32
Effective length of query: 391
Effective length of database: 410
Effective search space:   160310
Effective search space used:   160310
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