GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Actinomyces timonensis 7400942

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_017178740.1 A1QA_RS0109835 amino acid ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>NCBI__GCF_000295095.1:WP_017178740.1
          Length = 270

 Score =  156 bits (395), Expect = 5e-43
 Identities = 101/256 (39%), Positives = 146/256 (57%), Gaps = 27/256 (10%)

Query: 7   IAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIR 66
           IAG++K F +    + VLR VD+ V  G   +LVGPSG GKSTLL  I  L+    G + 
Sbjct: 19  IAGLHKFFDE----LHVLRGVDLTVPAGTVTVLVGPSGSGKSTLLRCINELESIDAGRVW 74

Query: 67  IGGKNVVGM---PPRD-----------------RDIAMVFQSYALYPTLSVADNIGFA-L 105
           + G+ ++GM   P RD                   I MVFQ + L+P ++   N+  A +
Sbjct: 75  VDGE-LIGMREVPGRDGTPVLHALSDKDRAAQRAKIGMVFQRFNLFPHMTALQNVMEAPV 133

Query: 106 EMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEP 165
            +++MPK + +KR  E+   + ++  +D  PSQLSGGQ+QRVA+ RALA  P+L LFDEP
Sbjct: 134 HVKRMPKEQARKRAAELLERVGLADRMDHYPSQLSGGQQQRVAIARALAMDPELMLFDEP 193

Query: 166 LSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDE 225
            S LD +L  E+ + +K L +  G+T V VTH+   A  +G ++  M GGVV + G P E
Sbjct: 194 TSALDPELVGEVLSVMKDLAR-DGMTMVVVTHEMGFAREVGDQLLFMDGGVVVERGVPSE 252

Query: 226 IYNRPANTYVATFIGS 241
           + +RPAN     F+ S
Sbjct: 253 VLDRPANERTRAFLSS 268


Lambda     K      H
   0.318    0.135    0.388 

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: 237
Number of extensions: 11
Number of successful extensions: 4
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: 355
Length of database: 270
Length adjustment: 27
Effective length of query: 328
Effective length of database: 243
Effective search space:    79704
Effective search space used:    79704
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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