GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araH in Dinoroseobacter shibae DFL-12

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)

Query= CharProtDB::CH_014278
         (328 letters)



>lcl|FitnessBrowser__Dino:3609042 Dshi_2431
           Monosaccharide-transporting ATPase (RefSeq)
          Length = 328

 Score =  175 bits (443), Expect = 2e-48
 Identities = 101/300 (33%), Positives = 161/300 (53%), Gaps = 4/300 (1%)

Query: 22  WDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSV 81
           W+   +LV   + F+A +   P F    N+       +   M+A  M   + SG+ DLSV
Sbjct: 23  WETLLLLVAIGI-FVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEIDLSV 81

Query: 82  ASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQI 141
           AS+IA A       + +       V  GL +G+LCG  NG ++ ++ + +++ T+ TM +
Sbjct: 82  ASIIALASTAMGAAVQMGVGTPGLVLIGLGVGLLCGAFNGVLVTRMGLPSIVVTIGTMSL 141

Query: 142 VRGLAYIISDGKAVGIEDESF--FALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRN 199
            RG++YI+   +A     ESF  F  GY  W+ +   + L     +I+ +LL+KT FGR 
Sbjct: 142 FRGISYIVLGDQAFRGYPESFSWFGQGYV-WWVISFELVLFAIIAVIYAMLLHKTNFGRA 200

Query: 200 TLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVI 259
             AIG N   A  +G+ V R K I+F+L+GL+S +A I L +R+ S +P  ++G+EL V+
Sbjct: 201 VYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSIAMGWELEVV 260

Query: 260 SACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDR 319
           +  VLGGVS+ GG G I  VV    ++G V   + LLN+      +V G +L+  +   R
Sbjct: 261 TMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSIVIGALLIGVIALPR 320


Lambda     K      H
   0.327    0.141    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: 328
Number of extensions: 31
Number of successful extensions: 3
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: 328
Length of database: 328
Length adjustment: 28
Effective length of query: 300
Effective length of database: 300
Effective search space:    90000
Effective search space used:    90000
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: 49 (23.5 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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