GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatY in Caldicellulosiruptor hydrothermalis 108

Align tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate WP_013402102.1 CALHY_RS00635 class II fructose-bisphosphate aldolase

Query= CharProtDB::CH_024465
         (286 letters)



>NCBI__GCF_000166355.1:WP_013402102.1
          Length = 278

 Score =  172 bits (435), Expect = 1e-47
 Identities = 98/282 (34%), Positives = 155/282 (54%), Gaps = 5/282 (1%)

Query: 3   IISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALEEI 62
           +++   +L   +   + V  FN  +A+  + +++   ++R P+I+         +  E I
Sbjct: 2   LVNLNEVLSYTKVKKFGVGMFNGLSADFYEGLIDAAEQLRCPIIIGVADRFVDRLDFEMI 61

Query: 63  YALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVD 122
             +    +   ++P+ +HLDH +SL +I R + AG  S M DGS  PF EN+K  K +V+
Sbjct: 62  AEVMIFLAKRASVPVCVHLDHAKSLKNIMRAIKAGFTSVMFDGSSLPFEENIKRTKEIVE 121

Query: 123 FCHSQDCSVEAELGRLGGVEDDMSVDAESAFLTDPQEAKRFVELTGVDSLAVAIGTAHGL 182
             HS   SVE ELG +G  + D        F T P EA+ F + T VD+LAV+IGT HG+
Sbjct: 122 IAHSVGVSVEGELGVVGRGDFDFK---NPEFYTKPDEAEEFAQKTQVDALAVSIGTVHGV 178

Query: 183 YSKTPKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRRTIELGVTKVNVATELKIAFAGA 242
           Y   PK+DF+RL+EIR+ VD  LVLHG S + DE  ++ IE G+ KVN+ T+L +A   A
Sbjct: 179 YKGEPKLDFERLSEIRKRVDCYLVLHGGSGLSDEDFKKCIEYGINKVNIFTDLTLAI-NA 237

Query: 243 VKAWFAENPQGNDPRYYMRVGMDAMKEVVRNKINVCGSANRI 284
               F +  +   P  + ++  + +K+    K+ + GS N I
Sbjct: 238 QLPEFIKQTEDLTPAIFEKI-REIVKQEAIKKLKIFGSYNII 278


Lambda     K      H
   0.319    0.134    0.386 

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: 179
Number of extensions: 7
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: 286
Length of database: 278
Length adjustment: 26
Effective length of query: 260
Effective length of database: 252
Effective search space:    65520
Effective search space used:    65520
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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