GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Desulfacinum infernum DSM 9756

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate WP_073037062.1 BUB04_RS03725 enoyl-CoA hydratase-related protein

Query= metacyc::MONOMER-18320
         (256 letters)



>NCBI__GCF_900129305.1:WP_073037062.1
          Length = 263

 Score =  149 bits (376), Expect = 6e-41
 Identities = 95/259 (36%), Positives = 136/259 (52%), Gaps = 6/259 (2%)

Query: 1   MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59
           M F  ILFE +D VA IT N P + N L    ++E+  A+   + D  ++++V   AGDK
Sbjct: 1   MDFQNILFEVRDGVALITFNRPKALNALNPQTLEELARAVAAARDDDAVRVVVLTGAGDK 60

Query: 60  AFCDGVDVADHV---PEKVDEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCD 116
           AF  G D+ +     P +          +F ++  +    +  VNG +LGGGCEL   CD
Sbjct: 61  AFVAGADITELQKMNPLEARLFAQKGQDVFFSLEDLPKPVIACVNGFALGGGCELAMSCD 120

Query: 117 IVIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVN 175
            + AS+KAK GQPEINL + P         +++G  KA EL +TG++I A++A+ +GLV 
Sbjct: 121 FIYASDKAKFGQPEINLGIIPGFGGTQRLARLVGRAKAKELCMTGEMIDAQQAKELGLVA 180

Query: 176 VVLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMAT 235
            V P E   E   K      +KS       +  +  G++ D L+   A E      C A 
Sbjct: 181 KVFPHEALLEETLKAATAMAAKSCTALRAIKHVVDRGMDAD-LKTGCALEAEAFGVCFAG 239

Query: 236 EDANEGLASFLEKRKPVFK 254
           +DA EG  +FLEKRKPVFK
Sbjct: 240 QDAKEGTTAFLEKRKPVFK 258


Lambda     K      H
   0.322    0.136    0.401 

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: 158
Number of extensions: 8
Number of successful extensions: 5
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: 256
Length of database: 263
Length adjustment: 24
Effective length of query: 232
Effective length of database: 239
Effective search space:    55448
Effective search space used:    55448
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: 47 (22.7 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