GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ctfB in Collimonas arenae Ter10

Align Butyrate--acetoacetate CoA-transferase subunit B; Short=Coat B; EC 2.8.3.9 (characterized, see rationale)
to candidate WP_061533759.1 CAter10_RS13185 CoA transferase subunit B

Query= uniprot:P23673
         (221 letters)



>NCBI__GCF_001584165.1:WP_061533759.1
          Length = 217

 Score =  187 bits (476), Expect = 1e-52
 Identities = 90/210 (42%), Positives = 140/210 (66%), Gaps = 5/210 (2%)

Query: 9   KEIIAKRVARELKNGQLVNLGVGLPTMVADYIPKNFKITFQSENGIVGMGASPKINEADK 68
           ++ +A R A+EL++G  VNLG+GLPT+VA+++P+  ++  QSENG++G+G  P  +  D 
Sbjct: 5   RDEMAARAAKELQDGFYVNLGIGLPTLVANHVPQEIEVWLQSENGLLGIGPFPTDDAVDP 64

Query: 69  DVVNAGGDYTTVLPDGTFFDSSVSFSLIRGGHVDVTVLGALQVDEKGNIANWIVPGKMLS 128
           D++NAG    T LP  ++F S+ SF++IRGG +++ +LGA+QV + G++ANW++PGKM+ 
Sbjct: 65  DLINAGKQTVTSLPGSSYFSSADSFAMIRGGKINIAILGAMQVSKNGDLANWMIPGKMVK 124

Query: 129 GMGGAMDLVNGAKKVIIAMRHTNKGQP-----KILKKCTLPLTAKSQANLIVTELGVIEV 183
           GMGGAMDLV G  +V++ M H  K +      KIL  C+LPLT     N I+T+LGV++V
Sbjct: 125 GMGGAMDLVAGVGRVVVLMEHVAKAKDGSTSHKILDACSLPLTGVGVVNRIITDLGVLDV 184

Query: 184 INDGLLLTEINKNTTIDEIRSLTAADLLIS 213
              GL + E+    +  +I   T   L +S
Sbjct: 185 TPQGLKVIELAPGVSQQDIIEQTGTPLDVS 214


Lambda     K      H
   0.316    0.136    0.376 

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: 178
Number of extensions: 9
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: 221
Length of database: 217
Length adjustment: 22
Effective length of query: 199
Effective length of database: 195
Effective search space:    38805
Effective search space used:    38805
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: 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