GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gatY in Collinsella tanakaei YIT 12063

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_009140764.1 HMPREF9452_RS03670 class II fructose-bisphosphate aldolase

Query= SwissProt::Q9KIP8
         (286 letters)



>NCBI__GCF_000225705.1:WP_009140764.1
          Length = 282

 Score =  244 bits (622), Expect = 2e-69
 Identities = 127/281 (45%), Positives = 174/281 (61%), Gaps = 1/281 (0%)

Query: 3   IISTKYLLQDAQANGYAVPAFNIHNAETIQAILEVCSEMRSPVILAGTPGTFKHIALEEI 62
           +++TK +L DAQ N YAV AFN+ N E + A+L    E +SPVI+  T GT K   L+  
Sbjct: 2   LVTTKEMLLDAQKNHYAVGAFNVENLEFVMAVLAAAEETKSPVIMQTTSGTIKKTGLDYF 61

Query: 63  YALCSAYSTTYNMPLALHLDHHESLDDIRRKVHAGVRSAMIDGSHFPFAENVKLVKSVVD 122
           Y +  A +   ++P+ALHLDH +  D   + +  G  S MIDGSH  F +N+ L K V D
Sbjct: 62  YGMVKAAAERASVPVALHLDHGDGYDRCMKALRTGYTSVMIDGSHETFEDNIALTKLVAD 121

Query: 123 FCHSQDCSVEAELGRLGGVEDDMSVDAESAFLTDPQEAKRFVELTGVDSLAVAIGTAHGL 182
              +    VEAELG++GG EDD+ V+ ES + TDP EAK FVE TG  SLA+ +GTAHG+
Sbjct: 122 AGAAMGIPVEAELGKVGGKEDDVEVEGESPY-TDPVEAKEFVERTGCTSLAIGVGTAHGV 180

Query: 183 YSKTPKIDFQRLAEIREVVDVPLVLHGASDVPDEFVRRTIELGVTKVNVATELKIAFAGA 242
           Y++ P ID   +  IR  VDVPLVLHG S VPDE V   ++ G+ KVN ATEL+ A+   
Sbjct: 181 YTEEPHIDQDVVKAIRAAVDVPLVLHGTSGVPDEQVAEAVKNGICKVNYATELRQAYTKG 240

Query: 243 VKAWFAENPQGNDPRNYMRVGMDAMKEVVRNKINVCGSANR 283
             A+ AENP   DP+N  + G + + ++V+ ++   GS  R
Sbjct: 241 YMAYMAENPNNFDPKNPGKAGAEEITKIVKIRMENLGSVGR 281


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: 217
Number of extensions: 11
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: 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.

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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