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_0592 N515DRAFT_0592 glucose/galactose transporter

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0592
          Length = 430

 Score =  220 bits (561), Expect = 6e-62
 Identities = 142/430 (33%), Positives = 230/430 (53%), Gaps = 19/430 (4%)

Query: 6   NTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQ 65
           +TS       +  +G     ++ L  LFF++GF+T LN  LI  +K  FSL+   A L+ 
Sbjct: 3   STSFAAGDTHDRASGLVPMLIIGL--LFFIFGFVTWLNGPLITFVKLAFSLDDVNAFLVP 60

Query: 66  FCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVL 125
             F+ +YF +++P+  ++KR G +KG+  GL + +IG  LF    S   YG  L  LFV+
Sbjct: 61  MVFYCSYFFLALPSSAVLKRTGMKKGMALGLFVMAIGAVLFGQFVSMRVYGGALAGLFVI 120

Query: 126 ASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILS-------- 177
            +G+ +LQ A+NPY++ LG  ++A+ R+      N +   +APF    L+LS        
Sbjct: 121 GAGLALLQTASNPYISILGPIDSAAQRIAFMGICNKVAGALAPFVFGWLVLSGIDTFDQQ 180

Query: 178 VAASVSSELAQA--NAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQT 235
           V A+ + E  +A  N  A  V +PYL +A  L +LA+   +  LP I+     A  E + 
Sbjct: 181 VKAAPTPEAREALLNTFAAKVHMPYLAMAGLLVLLAVWVLRSPLPEIK--PSGANSEAEI 238

Query: 236 HLGKTSALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWG 295
              K + L   HL LG + +F+YVG EV  G  +  + G+   +G+P +   H+ ++   
Sbjct: 239 GHAKGNLLSFPHLWLGVLCLFLYVGVEVMAGDAIGTY-GQG--LGLPLDATKHFTSFTLF 295

Query: 296 GAMVGRFIGSAVMQK-IPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMF 354
             ++G   G  ++ K I   + LA +A +     + A  T+G  ++  +  +G  N++M+
Sbjct: 296 AMLLGYLAGLVLIPKIISQQSYLAVSAVLGVAFTVGAWATTGYTSVGFVAALGFANAMMW 355

Query: 355 PTIFSLALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVV-CYGFI 413
           P IF LA++ LG  T  GS +L +AIVGGA+VP     L  +   QL F+L +V CY +I
Sbjct: 356 PAIFPLAIKGLGRWTEAGSALLIMAIVGGALVPQAFVHLKQHYDFQLVFMLLMVPCYLYI 415

Query: 414 LFYGAKGSKM 423
           LFYG +G ++
Sbjct: 416 LFYGLRGHRV 425


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: 486
Number of extensions: 34
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: 430
Length adjustment: 32
Effective length of query: 391
Effective length of database: 398
Effective search space:   155618
Effective search space used:   155618
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