GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Sm in Dyella japonica UNC79MFTsu3.2

Align MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)

Query= TCDB::Q8DT26
         (278 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3133
          Length = 273

 Score =  142 bits (358), Expect = 8e-39
 Identities = 87/269 (32%), Positives = 152/269 (56%), Gaps = 8/269 (2%)

Query: 12  IYALLILLSFIWLFPIIWVILTSFR--GEGTAYVPYIIPKTWTLDNYIKLFTNSSFPFGR 69
           +  LLI  + + +FP++W++  SF   GE +A  P ++P   TL NY +LF  +    GR
Sbjct: 10  VNGLLIGSTLVAVFPLLWMLSVSFMRPGEASALPPPLLPTHATLANYHELFERAGM--GR 67

Query: 70  WFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAVYYI 129
           + LN+L VS+A  +LS +  +   Y+ ++++F  R    ++ L   + P  ++M+ ++ +
Sbjct: 68  YLLNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLL 127

Query: 130 LKALNLTQTLTSLVLVYSSGAALTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKITLP 189
           LK L L  +  ++V V +       ++ + +   IP  L E+A IDGA    IF++I LP
Sbjct: 128 LKYLGLVNSYAAVV-VPAMATIFGIFLVRQYARGIPDDLMEAARIDGAGELRIFVQIVLP 186

Query: 190 LSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTINNWFMAFAAG 249
           L KPI+V  A+  F+  W DF++  + L      YT+ I L S+ +    ++  M   AG
Sbjct: 187 LLKPIMVTLAIFTFLTAWNDFMWPLIAL-TGQEHYTLPIALASLSREHVQDSELM--MAG 243

Query: 250 SVLIAIPITILFIFMQKYYVEGITGGSVK 278
           SV+  +P+ +LF+ +Q+YY++G+  GSVK
Sbjct: 244 SVVTVLPVLVLFLALQRYYLQGLLLGSVK 272


Lambda     K      H
   0.330    0.142    0.428 

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: 190
Number of extensions: 13
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: 278
Length of database: 273
Length adjustment: 25
Effective length of query: 253
Effective length of database: 248
Effective search space:    62744
Effective search space used:    62744
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 (21.8 bits)
S2: 47 (22.7 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