GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoA in Rhodococcus qingshengii djl-6-2

Align acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8) (characterized)
to candidate WP_042453492.1 C1M55_RS06025 CoA transferase subunit A

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



>NCBI__GCF_002893965.1:WP_042453492.1
          Length = 251

 Score =  256 bits (653), Expect = 4e-73
 Identities = 135/244 (55%), Positives = 166/244 (68%), Gaps = 19/244 (7%)

Query: 4   IYPSAAHALEGLVEDGMTIAVGGFGLCGIPEQLIAALRDSGKKDLTAISNNAGVDGFGLG 63
           +Y SAA A+  +V DG T+AVGGFGLCGIP+ LI A+  +    L   SNN GVD  GLG
Sbjct: 1   MYESAAEAVADIV-DGATLAVGGFGLCGIPDVLIDAIAATSATHLEVFSNNCGVDDHGLG 59

Query: 64  LLLETRQISKMVSSYVGENKEFERQYLAGELALEFTPQGTLAEKLRAGGAGIPAFYTKTG 123
           +LL   +I ++ +SYVGENKEF RQYLAGEL +E TPQGTLAE+LRAGG GIPAF+T  G
Sbjct: 60  ILLSAGRIRRVTASYVGENKEFARQYLAGELEVELTPQGTLAERLRAGGTGIPAFFTPAG 119

Query: 124 YGTLVAEG------------------KETRQFNGEWYVMEESLTADLALVKAWKADKAGN 165
            G+ +++G                  KETR F  + YVMEE++ AD ALV A   D  GN
Sbjct: 120 VGSPISDGGMPWRYDADGSIAIASPPKETRVFGTKRYVMEEAINADYALVHAVLGDTDGN 179

Query: 166 LLFRKTARNFNPLAAMAGEVCVVEVEEIVETGELDPDQIHLPGIYVHRIVHNPNPEKRIE 225
           L+F KTA NFNPLAAMAG V + +VE +VE GE+DP  +HLPG++V R+VH     KRIE
Sbjct: 180 LVFDKTAMNFNPLAAMAGRVTIAQVERLVEPGEIDPASVHLPGVFVQRVVHTGPQNKRIE 239

Query: 226 KRTV 229
           KRTV
Sbjct: 240 KRTV 243


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: 196
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: 231
Length of database: 251
Length adjustment: 23
Effective length of query: 208
Effective length of database: 228
Effective search space:    47424
Effective search space used:    47424
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 24 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