GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Cupriavidus basilensis 4G11

Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate RR42_RS22970 RR42_RS22970 3-oxoadipate CoA-transferase

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



>FitnessBrowser__Cup4G11:RR42_RS22970
          Length = 230

 Score =  192 bits (488), Expect = 5e-54
 Identities = 99/216 (45%), Positives = 140/216 (64%), Gaps = 4/216 (1%)

Query: 5   DKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVDGFGL 64
           +KRV+S  EA+  L+DG TV+ GGFG  G+P+ LIA +   G RDLTV+SNN G DG G+
Sbjct: 3   NKRVASCAEAIADLRDGATVMVGGFGSAGLPDGLIAAVLAHGARDLTVISNNAGYDGEGV 62

Query: 65  GVLLEDRQIRKVVASY---VGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAFF 121
             L+E  ++RK+V SY    G  A F      GE+E+ L  QGTL E++R  GAG+  F+
Sbjct: 63  ASLIEAGRMRKLVCSYPLTAGATA-FRDAYRRGEVELELVAQGTLVERIRCAGAGLGGFY 121

Query: 122 TATGVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLA 181
                GT +A+GK+ RE +G  +++E  +  DFA+++G  AD  GN+ Y    +NFNP+ 
Sbjct: 122 CPITAGTILAQGKDTREINGVLHVLELPLHADFALIRGRHADRLGNLDYHLAGRNFNPIM 181

Query: 182 ATAGKITVVEVEEIVEPGELDPTQIHTPGIYVDRVI 217
           ATA ++ V EVE +VE G ++P QI TPGI+V RV+
Sbjct: 182 ATAARVVVAEVEAMVEAGAMNPEQIVTPGIFVHRVV 217


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: 159
Number of extensions: 7
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: 230
Length adjustment: 23
Effective length of query: 209
Effective length of database: 207
Effective search space:    43263
Effective search space used:    43263
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