GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS16145 BWI76_RS16145 3-oxoadipate
           CoA-transferase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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