GapMind for catabolism of small carbon sources

 

Alignments for a candidate for catI in Methylocapsa aurea KYG

Align 3-oxoadipate CoA-transferase subunit A; 3-oxoadipate:succinyl-CoA transferase subunit A; Beta-ketoadipate:succinyl-CoA transferase subunit A; EC 2.8.3.6 (characterized)
to candidate WP_036258219.1 DL86_RS03250 CoA-transferase

Query= SwissProt::Q8VPF3
         (282 letters)



>NCBI__GCF_000746085.1:WP_036258219.1
          Length = 320

 Score =  126 bits (317), Expect = 5e-34
 Identities = 87/273 (31%), Positives = 136/273 (49%), Gaps = 8/273 (2%)

Query: 15  VNDGDTVALEG-FTHLIPTAASHEIIRQGKKDLHLVRMTPDLVYDLLIGAGCARKLTFSW 73
           V DG  VA+ G  +   P A    I+R+G K L +V     +  DLL G G   + + S+
Sbjct: 26  VKDGSVVAVGGGLSSREPMALLRAILRRGVKGLTVVGSAHGIDIDLLSGGGAISRSSESY 85

Query: 74  GG-NPGVGSLHRLRDAVEKGWPNALEIDEHSHADLANSYVAGASGLPFAVLRAYAGSDLP 132
            G     G     R A+E G   A+ +D+     L     A   GLPF  +R+  G+  P
Sbjct: 86  VGFEQDFGMAPNYRRALESG---AVSVDDSCCYTLVQQLRAAIQGLPFLPIRSVRGTSFP 142

Query: 133 KVNPNIKFINCPFTGEQLAAVPSVRPDVTVIHAQKADRKGNVLLWGILGVQKEAALAAKR 192
            ++P  K + CPFTGE+L  VP++ P+V +IHAQ  D +GN+L+ G        A A++ 
Sbjct: 143 SLHPEYKRMICPFTGEELLLVPAIEPEVALIHAQYGDAQGNLLIQGPPVADILFAKASRE 202

Query: 193 CIVTVEEIVDDLN-APMNSCVLPTWALSAVCHVPGGSHPSYAHGYYERDNRFYQAWDPIA 251
            + TVEEIV       +    +P + ++AV  VP G+HP+  + +Y  D R    +   A
Sbjct: 203 VLATVEEIVSTARLKELGGVSIPYFYVTAVSEVPMGAHPTACYPFYAYDRRHTVLYYEAA 262

Query: 252 R-DRETFTA-WIDEYIRGTKDFSEFQAKIAEGK 282
           R   + F A ++  ++ G  D +++ A+I   K
Sbjct: 263 RKGADAFLAEYLSVFVHGAPDHADYLAQIGGEK 295


Lambda     K      H
   0.320    0.136    0.424 

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: 235
Number of extensions: 13
Number of successful extensions: 3
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: 282
Length of database: 320
Length adjustment: 27
Effective length of query: 255
Effective length of database: 293
Effective search space:    74715
Effective search space used:    74715
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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