GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoD in Sphingomonas koreensis DSMZ 15582

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate Ga0059261_0263 Ga0059261_0263 3-oxoacid CoA-transferase, B subunit

Query= reanno::psRCH2:GFF1044
         (209 letters)



>FitnessBrowser__Korea:Ga0059261_0263
          Length = 216

 Score =  282 bits (721), Expect = 4e-81
 Identities = 137/205 (66%), Positives = 167/205 (81%), Gaps = 2/205 (0%)

Query: 1   MAWTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEE 60
           M WTR++MA RAA+EL+DGFYVNLGIG+PTLVAN+IPEG++V LQSENG+LGIGPFP E 
Sbjct: 1   MPWTRDEMAARAAKELRDGFYVNLGIGIPTLVANHIPEGVEVTLQSENGMLGIGPFPYEG 60

Query: 61  EIDPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG 120
           E DPDLINAGKQT++ LP S +F +A SFAMIRGGHI+L +LGAM+V++ GD+ANWMIPG
Sbjct: 61  EEDPDLINAGKQTISELPQSVYFSSADSFAMIRGGHIDLTVLGAMEVAQNGDIANWMIPG 120

Query: 121 KMVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDV 180
           KM+KGMGGAMDLVAGVK+++V+MEH AK G  K +P C LPLTG  VVD IITDL V   
Sbjct: 121 KMIKGMGGAMDLVAGVKKIIVVMEHNAKDGTPKFIPECTLPLTGKNVVDMIITDLAVFQR 180

Query: 181 TEQG--LKLVELAEGVSFDELQEAT 203
            +     +L+ELA GV+ +EL   T
Sbjct: 181 ADHDSPFRLIELAPGVTEEELAAKT 205


Lambda     K      H
   0.318    0.138    0.404 

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: 6
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: 209
Length of database: 216
Length adjustment: 21
Effective length of query: 188
Effective length of database: 195
Effective search space:    36660
Effective search space used:    36660
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 (21.7 bits)
S2: 45 (21.9 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