GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609042
          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 (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