GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoA in Pseudomonas putida KT2440

Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate PP_3122 PP_3122 acetoacetyl CoA-transferase (subunit A)

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



>lcl|FitnessBrowser__Putida:PP_3122 PP_3122 acetoacetyl
           CoA-transferase (subunit A)
          Length = 232

 Score =  404 bits (1037), Expect = e-117
 Identities = 196/231 (84%), Positives = 220/231 (95%)

Query: 1   MAGFDKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVD 60
           MAG DKRV++YE+ALEGL D MTV+AGGFGLCGIPENLI+EIKR+G++ LTVVSNNCGVD
Sbjct: 1   MAGLDKRVATYEQALEGLTDNMTVLAGGFGLCGIPENLISEIKRRGVKGLTVVSNNCGVD 60

Query: 61  GFGLGVLLEDRQIRKVVASYVGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAF 120
           GFGLGVLLEDRQIRK++ASYVGENA FE+QLLSGE+EV LTPQGTLAEKMRAGGAGIPAF
Sbjct: 61  GFGLGVLLEDRQIRKMIASYVGENAEFERQLLSGELEVELTPQGTLAEKMRAGGAGIPAF 120

Query: 121 FTATGVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPL 180
           +TATG GTPVA+GKEVREF GR+Y++EESITGDFAIVKGWKADH+GNV+YR+TAQNFNPL
Sbjct: 121 YTATGYGTPVADGKEVREFKGRKYILEESITGDFAIVKGWKADHYGNVVYRNTAQNFNPL 180

Query: 181 AATAGKITVVEVEEIVEPGELDPTQIHTPGIYVDRVICGTFEKRIEQRTVR 231
           AATAGKITVVEVEEIVEPG L P++IHTPGIYVDRVI GTFEKRIE+RTV+
Sbjct: 181 AATAGKITVVEVEEIVEPGVLLPSEIHTPGIYVDRVIVGTFEKRIEKRTVK 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: 286
Number of extensions: 6
Number of successful extensions: 1
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: 232
Length adjustment: 23
Effective length of query: 209
Effective length of database: 209
Effective search space:    43681
Effective search space used:    43681
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 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, 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