GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoD in Streptacidiphilus oryzae TH49

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate WP_037571199.1 BS73_RS10020 CoA transferase subunit B

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



>NCBI__GCF_000744815.1:WP_037571199.1
          Length = 214

 Score =  308 bits (790), Expect = 4e-89
 Identities = 147/208 (70%), Positives = 178/208 (85%)

Query: 1   MAWTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEE 60
           MAWTRE+MA RAA+EL DG YVNLGIGLPTL+ NY+PEG++V L+SENGLLG+GP+PTE+
Sbjct: 1   MAWTREEMAARAARELPDGAYVNLGIGLPTLIPNYLPEGVEVILESENGLLGVGPYPTED 60

Query: 61  EIDPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG 120
           E+DPDLINAGK+TVT LPGSSFFD++ SF MIRGGHI+ A+LGAM+VS +GDLANW IPG
Sbjct: 61  EVDPDLINAGKETVTVLPGSSFFDSSLSFGMIRGGHIDAAVLGAMEVSARGDLANWAIPG 120

Query: 121 KMVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDV 180
           KM+KGMGGAMDLV G ++V+VL  H AK G+ KI+  C LPLTG G VDR+ITDLGVLDV
Sbjct: 121 KMIKGMGGAMDLVHGARQVIVLTTHNAKDGSPKIVEECSLPLTGKGCVDRVITDLGVLDV 180

Query: 181 TEQGLKLVELAEGVSFDELQEATGSPIQ 208
           TE GL LVE A GV+ +E+ E TG+P++
Sbjct: 181 TESGLVLVETAPGVTPEEVVERTGAPVR 208


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: 236
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: 209
Length of database: 214
Length adjustment: 21
Effective length of query: 188
Effective length of database: 193
Effective search space:    36284
Effective search space used:    36284
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 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