GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoD in Herbaspirillum seropedicae SmR1

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate HSERO_RS23185 HSERO_RS23185 succinyl-CoA:3-ketoacid-CoA transferase

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



>FitnessBrowser__HerbieS:HSERO_RS23185
          Length = 216

 Score =  321 bits (822), Expect = 7e-93
 Identities = 160/211 (75%), Positives = 184/211 (87%), Gaps = 4/211 (1%)

Query: 1   MAWTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEE 60
           MAWTR++MA RAA+ELQDGFYVNLGIGLPTLVAN++P  ++VWLQSENGLLGIGPFPTE+
Sbjct: 1   MAWTRDEMAARAAKELQDGFYVNLGIGLPTLVANHVPSDIEVWLQSENGLLGIGPFPTED 60

Query: 61  EIDPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG 120
           ++DPDLINAGKQTVT +PGSSFF +A SF MIRGG IN+AILGAMQVS KGDLANWMIPG
Sbjct: 61  QVDPDLINAGKQTVTTIPGSSFFSSADSFGMIRGGKINIAILGAMQVSAKGDLANWMIPG 120

Query: 121 KMVKGMGGAMDLVAGVKRVVVLMEHTAK----GGAHKILPACDLPLTGLGVVDRIITDLG 176
           KMVKGMGGAMDLVAGV RVVVLMEH AK      + KIL  C+LPLTG+GVV+RIITDLG
Sbjct: 121 KMVKGMGGAMDLVAGVGRVVVLMEHVAKAKDGSTSKKILNDCNLPLTGVGVVNRIITDLG 180

Query: 177 VLDVTEQGLKLVELAEGVSFDELQEATGSPI 207
           V+DVT  GLKL+ELA GV+ +E+ E T +P+
Sbjct: 181 VIDVTPGGLKLIELASGVTKEEVIEKTEAPL 211


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: 252
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