GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Klebsiella michiganensis M5al

Align Succinyl-CoA:3-ketoacid coenzyme A transferase subunit A; Succinyl-CoA:3-oxoacid CoA-transferase; OXCT A; EC 2.8.3.5 (characterized)
to candidate BWI76_RS16145 BWI76_RS16145 3-oxoadipate CoA-transferase

Query= SwissProt::P56006
         (232 letters)



>FitnessBrowser__Koxy:BWI76_RS16145
          Length = 228

 Score =  202 bits (514), Expect = 4e-57
 Identities = 97/219 (44%), Positives = 147/219 (67%), Gaps = 2/219 (0%)

Query: 1   MNKVITDLDKALSALKDGDTILVGGFGLCGIPEYAIDYIYKKGIKDLIVVSNNCGVDDFG 60
           ++K ++ L  A++ + DG TI++GGFG  G P Y ID + ++G +DL +++NN G  + G
Sbjct: 2   IDKSVSTLRDAIAGIHDGATIMIGGFGPAGQPTYLIDALIEQGARDLTIINNNAGNGEVG 61

Query: 61  LGILLEKKQIKKIIASYVGE--NKIFESQMLNGEIEVVLTPQGTLAENLHAGGAGIPAYY 118
           L  LL+  +++K+I S+  +  ++IF+     G++E+ L PQG LA  + A GAG+ A +
Sbjct: 62  LAALLKAGRVRKMICSFPRQVDSQIFDDLYRRGKVELELVPQGNLAARIQAAGAGLGAVF 121

Query: 119 TPTGVGTLIAQGKESREFNGKEYILERAITGDYGLIKAYKSDTLGNLVFRKTARNFNPLC 178
           TPTG GT +A+GKE+RE +G  Y+LE  I  D+ LIKA++ D  GNLV+RK ARNF P+ 
Sbjct: 122 TPTGYGTPLAEGKETREIDGHHYVLEYPIKADFALIKAHQGDRWGNLVYRKAARNFGPIM 181

Query: 179 AMAAKICVAEVEEIVPAGELDPDEIHLPGIYVQHIYKGE 217
           A AAK  + EV ++VP G LDP+ I  PGI+VQ ++  E
Sbjct: 182 ATAAKTTIVEVSQLVPLGSLDPESIITPGIFVQRVFSLE 220


Lambda     K      H
   0.317    0.140    0.400 

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: 163
Number of extensions: 8
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: 228
Length adjustment: 23
Effective length of query: 209
Effective length of database: 205
Effective search space:    42845
Effective search space used:    42845
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 (21.6 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