GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Shewanella oneidensis MR-1

Align Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A (characterized)
to candidate 201054 SO1892 acetate CoA-transferase, subunit A (NCBI ptt file)

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



>FitnessBrowser__MR1:201054
          Length = 234

 Score =  344 bits (883), Expect = e-100
 Identities = 167/231 (72%), Positives = 194/231 (83%)

Query: 1   MAGFDKRVSSYEEALEGLKDGMTVIAGGFGLCGIPENLIAEIKRKGIRDLTVVSNNCGVD 60
           MAG +K VSSYEEAL GL D MT++ GGFGLCGIPE LI ++ + G++ LT +SNN GVD
Sbjct: 1   MAGLNKVVSSYEEALTGLSDDMTIMVGGFGLCGIPEGLINQMVKMGVKGLTAISNNAGVD 60

Query: 61  GFGLGVLLEDRQIRKVVASYVGENALFEQQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAF 120
            FGLG+LL+ RQI  ++ASYVGENA FEQQ+LSGE+ V+LTPQGTLAEK+RAGGAGIPAF
Sbjct: 61  DFGLGLLLKHRQISTMIASYVGENATFEQQMLSGELNVILTPQGTLAEKIRAGGAGIPAF 120

Query: 121 FTATGVGTPVAEGKEVREFHGRQYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPL 180
           FTATG GTPVAEGKE RE  GR Y++EES+T DFA+V+ WKAD  GN+++R TA NFNP+
Sbjct: 121 FTATGYGTPVAEGKETREIKGRHYVLEESLTADFALVRAWKADTMGNLVFRKTAANFNPM 180

Query: 181 AATAGKITVVEVEEIVEPGELDPTQIHTPGIYVDRVICGTFEKRIEQRTVR 231
            ATAGKITVVE E IVEPGELDP  IHTPGIYVDRVI G FEKRIEQRTV+
Sbjct: 181 MATAGKITVVEAEFIVEPGELDPDHIHTPGIYVDRVIQGKFEKRIEQRTVK 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: 225
Number of extensions: 4
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: 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