GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16925 in Dinoroseobacter shibae DFL-12

Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)

Query= uniprot:A0A161GM94
         (322 letters)



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

 Score =  162 bits (410), Expect = 1e-44
 Identities = 94/310 (30%), Positives = 165/310 (53%), Gaps = 3/310 (0%)

Query: 12  RKPLDLRRFLDDWVMLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCL 71
           R P++ R    + ++LL AIGIFV  +     FL+  N+       +   + A  M   +
Sbjct: 13  RSPMEQRLKSWETLLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLI 72

Query: 72  ASGHFDLSVGSVIACAGV-VAAVVMRDTNSVFLGISAALVMGLIVGLINGIVIAKLRVNA 130
            SG  DLSV S+IA A   + A V     +  L +   L +GL+ G  NG+++ ++ + +
Sbjct: 73  ISGEIDLSVASIIALASTAMGAAVQMGVGTPGL-VLIGLGVGLLCGAFNGVLVTRMGLPS 131

Query: 131 LITTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGV-PVPILITIVCFLFFGWL 189
           ++ T+ TM + RG++YI    +A     ESF  FG G ++ V    +++  +  + +  L
Sbjct: 132 IVVTIGTMSLFRGISYIVLGDQAFRGYPESFSWFGQGYVWWVISFELVLFAIIAVIYAML 191

Query: 190 LNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMI 249
           L+ T +GR   AIG N   A+ +G+ V R K I+F + G++  +A + L +R+ S +P I
Sbjct: 192 LHKTNFGRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLGSTRPSI 251

Query: 250 GQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSI 309
             G+EL V++  VLGGVS+ GG G I  V+    ++ ++   + L N+      ++ G++
Sbjct: 252 AMGWELEVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMSIVIGAL 311

Query: 310 LLLAVVIDRL 319
           L+  + + RL
Sbjct: 312 LIGVIALPRL 321


Lambda     K      H
   0.330    0.144    0.420 

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: 253
Number of extensions: 18
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: 322
Length of database: 328
Length adjustment: 28
Effective length of query: 294
Effective length of database: 300
Effective search space:    88200
Effective search space used:    88200
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: 48 (23.1 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