GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Caulobacter crescentus NA1000

Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate CCNA_02488 CCNA_02488 acetate/3-ketoacid CoA transferase, subunit A

Query= reanno::psRCH2:GFF1045
         (231 letters)



>FitnessBrowser__Caulo:CCNA_02488
          Length = 245

 Score =  300 bits (769), Expect = 1e-86
 Identities = 157/229 (68%), Positives = 177/229 (77%)

Query: 2   NKIYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGFG 61
           +KIY SAA ALEG+V DGMT+  GGFGL G PE LI AL+D+G K LT ISNN G DGFG
Sbjct: 7   SKIYESAAAALEGVVFDGMTLMSGGFGLSGNPETLIPALKDTGVKALTVISNNCGADGFG 66

Query: 62  LGLLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYTK 121
           L +LL   QI KMVSSYVGENK FE+ YL+GEL LE  PQGTLAE++RAGGAGIPAFYTK
Sbjct: 67  LWMLLNNGQIRKMVSSYVGENKLFEQLYLSGELELELNPQGTLAERIRAGGAGIPAFYTK 126

Query: 122 TGYGTLVAEGKETRQFNGEWYVMEESLTADLALVKAWKADKAGNLLFRKTARNFNPLAAM 181
           TG GT+VAEGK    F GE Y+ E  L ADL++VKAWKAD  GNL+FR TARNFNP+ A 
Sbjct: 127 TGVGTVVAEGKPVETFEGEPYLRETWLRADLSIVKAWKADPEGNLVFRMTARNFNPVMAT 186

Query: 182 AGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIEKRTVR 230
           AG+V +VEVEEIVE GELD + IH PGIYV RIV +   EKRIEK T R
Sbjct: 187 AGKVTIVEVEEIVEAGELDANAIHTPGIYVDRIVKSTINEKRIEKLTTR 235


Lambda     K      H
   0.316    0.135    0.391 

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: 217
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: 231
Length of database: 245
Length adjustment: 23
Effective length of query: 208
Effective length of database: 222
Effective search space:    46176
Effective search space used:    46176
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