GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Pedobacter sp. GW460-11-11-14-LB5

Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate CA265_RS06305 CA265_RS06305 succinyl-CoA--3-ketoacid-CoA transferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2111
         (232 letters)



>FitnessBrowser__Pedo557:CA265_RS06305
          Length = 234

 Score =  289 bits (740), Expect = 3e-83
 Identities = 141/229 (61%), Positives = 178/229 (77%), Gaps = 1/229 (0%)

Query: 5   DKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVDGFGL 64
           +K VS  EEA++ + DG+T++ GGFGLCGIPEN I  +  K +++LT +SNN GVD FG+
Sbjct: 3   NKVVSGAEEAIKDISDGVTLMLGGFGLCGIPENCIKALVNKQVKNLTCISNNAGVDDFGI 62

Query: 65  GVLLEDRQIRKVVASYVGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAFFTAT 124
           G++L+ RQ++K+++SYVGENA FE+QLLSGE+EV L PQGTLA +  A G G+PA FT  
Sbjct: 63  GLMLKQRQVKKMISSYVGENAEFERQLLSGELEVDLIPQGTLATRCLAAGYGMPAIFTPA 122

Query: 125 GVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLAATA 184
           GVGT VAEGKE+R F G+ YLME +   DFAIVK WK D  GN+I+R T++NFNP+ A A
Sbjct: 123 GVGTEVAEGKEIRNFDGKDYLMEYAFDADFAIVKAWKGDTAGNLIFRSTSRNFNPVMAMA 182

Query: 185 GKITVVEVEEIVEPGELDPTQIHTPGIYVDRVICG-TFEKRIEQRTVRK 232
           GKIT+ EVEE+VE GELDP  IHTPGIYV R+  G  +EKRIEQRTVRK
Sbjct: 183 GKITIAEVEELVEAGELDPDYIHTPGIYVHRIFQGKDYEKRIEQRTVRK 231


Lambda     K      H
   0.319    0.139    0.403 

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: 226
Number of extensions: 4
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: 232
Length of database: 234
Length adjustment: 23
Effective length of query: 209
Effective length of database: 211
Effective search space:    44099
Effective search space used:    44099
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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