GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Thiothrix lacustris DSM 21227

Align TreV, component of Trehalose porter (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  240 bits (612), Expect = 4e-68
 Identities = 128/282 (45%), Positives = 189/282 (67%), Gaps = 6/282 (2%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           +EL ++ K YGK   I  ++ +I++GEF V +GPSG GKSTLL+++AG+E ++ G++I D
Sbjct: 4   LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
           G DIT+ PP +R++AMVFQ+YALYP+M+V +N++F L++  +    I E+V+ AA  L +
Sbjct: 64  GRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADKLNL 123

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
           +  L +    +SGGQ+QRVA+ R+IVR+P  FL DEPLSNLDA +R   R E+  + +EL
Sbjct: 124 TAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLHREL 183

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFLP 242
             T +YVTHDQ EA++LADR+ +L  G  EQV  P  LY+ P  ++VA+F+G   MN  P
Sbjct: 184 GATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMNVAP 243

Query: 243 GELMKE---KAQEIGFRPEWVEV---GKGNLSCMVESVEASG 278
             L  +   +  E+G RPE +++     G L+  V  VEA G
Sbjct: 244 ASLFGQFPAQVAEVGIRPEHLQMVSPEDGLLAGKVVLVEALG 285


Lambda     K      H
   0.318    0.137    0.385 

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: 273
Number of extensions: 11
Number of successful extensions: 1
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: 324
Length of database: 348
Length adjustment: 28
Effective length of query: 296
Effective length of database: 320
Effective search space:    94720
Effective search space used:    94720
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: 49 (23.5 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