GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatY in Streptacidiphilus oryzae TH49

Align D-tagatose-1,6-bisphosphate aldolase subunit KbaY; TBPA; TagBP aldolase; D-tagatose-bisphosphate aldolase class II; Ketose 1,6-bisphosphate aldolase class II; Tagatose-bisphosphate aldolase; EC 4.1.2.40 (characterized)
to candidate WP_037573293.1 BS73_RS16635 class II fructose-bisphosphate aldolase family protein

Query= SwissProt::Q9KIP8
         (286 letters)



>NCBI__GCF_000744815.1:WP_037573293.1
          Length = 282

 Score =  176 bits (445), Expect = 7e-49
 Identities = 104/279 (37%), Positives = 150/279 (53%), Gaps = 2/279 (0%)

Query: 1   MSIISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGT--FKHIA 58
           MS++ T+ L+  A A G A  AFN+   E  +AI    S   + VIL  +     F    
Sbjct: 1   MSLVPTRDLVSKAAAAGRAAAAFNVITLEHAEAITAGASAAGTAVILQISENAVRFHGGR 60

Query: 59  LEEIYALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVK 118
           +  I    +  +   ++ +ALHLDH   L  +     AG  SAM D    P+AEN+   +
Sbjct: 61  VSPIARAAAEVARGCDVDVALHLDHVTDLRLLHTAAEAGFSSAMFDAGAQPYAENLAATR 120

Query: 119 SVVDFCHSQDCSVEAELGRLGGVEDDMSVDAESAFLTDPQEAKRFVELTGVDSLAVAIGT 178
           +   + H     +EAELG +GG  D  +    +   TDP+EA  +V  TGVD+LAVA+G+
Sbjct: 121 AAAQWAHGAGVWLEAELGYVGGKPDAPASAHAAGVRTDPREAAAYVADTGVDALAVAVGS 180

Query: 179 AHGLYSKTPKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRRTIELGVTKVNVATELKIA 238
           +H +  ++  +D + +  +R+ V VPLVLHG+S V D+ +RR +  G+ KVNV T L IA
Sbjct: 181 SHAMTERSAALDHELIGRLRDAVPVPLVLHGSSGVGDDELRRAVRAGIAKVNVGTALNIA 240

Query: 239 FAGAVKAWFAENPQGNDPRNYMRVGMDAMKEVVRNKINV 277
           F  AV+   AE P   DPR Y+  G DAM E VR  + V
Sbjct: 241 FTRAVRETLAEKPDLTDPRGYLAPGRDAMAETVRALLGV 279


Lambda     K      H
   0.319    0.133    0.384 

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: 190
Number of extensions: 7
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: 286
Length of database: 282
Length adjustment: 26
Effective length of query: 260
Effective length of database: 256
Effective search space:    66560
Effective search space used:    66560
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