GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Desulfacinum infernum DSM 9756

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_073037062.1 BUB04_RS03725 enoyl-CoA hydratase-related protein

Query= reanno::Cup4G11:RR42_RS28545
         (384 letters)



>NCBI__GCF_900129305.1:WP_073037062.1
          Length = 263

 Score = 90.5 bits (223), Expect = 5e-23
 Identities = 80/273 (29%), Positives = 121/273 (44%), Gaps = 24/273 (8%)

Query: 23  VRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAG 82
           + F+  +G+ LIT NRP+ LNAL+   +  L   +AA    D +  VVL GAG KAF AG
Sbjct: 6   ILFEVRDGVALITFNRPKALNALNPQTLEELARAVAAARDDDAVRVVVLTGAGDKAFVAG 65

Query: 83  GDIRALYDSFHAGTALHRQFFVDEYQ-LDYRLHCYPKPVVALMDGIVMGGGMGLAQAAHL 141
            DI  L         L  + F  + Q + + L   PKPV+A ++G  +GGG  LA +   
Sbjct: 66  ADITELQKM----NPLEARLFAQKGQDVFFSLEDLPKPVIACVNGFALGGGCELAMSCDF 121

Query: 142 RVLTERSRVAMPETGIGLVPDVGASHFLSKL-PLALALYVGLTGVTLGAADTLLCKLADI 200
              +++++   PE  +G++P  G +  L++L   A A  + +TG  + A       L   
Sbjct: 122 IYASDKAKFGQPEINLGIIPGFGGTQRLARLVGRAKAKELCMTGEMIDAQQAKELGLVAK 181

Query: 201 AVPAASLEHFEQTLAAINRTGDVLADLRAALQATPDAGEQAAPLQSVLPAVLRHFRADAS 260
             P  +L   E+TL A                AT  A +    L+++   V R   AD  
Sbjct: 182 VFPHEAL--LEETLKA----------------ATAMAAKSCTALRAIKHVVDRGMDADLK 223

Query: 261 VAGLLDSLAAESDPAYADWAARTLDILRGRSPL 293
               L++ A     A  D    T   L  R P+
Sbjct: 224 TGCALEAEAFGVCFAGQDAKEGTTAFLEKRKPV 256


Lambda     K      H
   0.322    0.137    0.405 

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: 165
Number of extensions: 7
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: 384
Length of database: 263
Length adjustment: 27
Effective length of query: 357
Effective length of database: 236
Effective search space:    84252
Effective search space used:    84252
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 (21.9 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