GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Malonomonas rubra DSM 5091

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV

Query= TCDB::G3LHY8
         (358 letters)



>NCBI__GCF_900142125.1:WP_072908814.1
          Length = 415

 Score =  122 bits (307), Expect = 1e-32
 Identities = 73/240 (30%), Positives = 131/240 (54%), Gaps = 9/240 (3%)

Query: 26  RGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGM------PVQKRNVAMVY 79
           +G + V++G + +GK++++R++  L  PT G +  DG D+  M       V++  ++MV+
Sbjct: 55  KGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLSMVF 114

Query: 80  QQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQR 139
           Q F   P +TV  N A  + + G D  T ++   +A E + L  + +  P  LSGG QQR
Sbjct: 115 QSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGMQQR 174

Query: 140 TALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLG 199
             LAR L  +  ++LMDE  + LD  +R E+++EL K+ A++    V+ + +  EA+ +G
Sbjct: 175 VGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAMRIG 234

Query: 200 GNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDVTKSGNVFTRPSGVTIPV 259
              A +  GRV Q G   E+ + P +      F    ++  ++  +G++ T+ + VTIP+
Sbjct: 235 DRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRG--VDPTNILTAGDIATQ-TQVTIPI 291


Lambda     K      H
   0.319    0.136    0.392 

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: 310
Number of extensions: 9
Number of successful extensions: 2
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: 358
Length of database: 415
Length adjustment: 30
Effective length of query: 328
Effective length of database: 385
Effective search space:   126280
Effective search space used:   126280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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