GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudarthrobacter sulfonivorans Ar51

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate WP_058930224.1 AU252_RS07800 enoyl-CoA hydratase

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



>NCBI__GCF_001484605.1:WP_058930224.1
          Length = 258

 Score =  149 bits (377), Expect = 4e-41
 Identities = 94/255 (36%), Positives = 138/255 (54%), Gaps = 7/255 (2%)

Query: 3   FNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAF 61
           +  IL E++ +V  +TLN P + N L    M ++  A+  +  DP +  +V      KAF
Sbjct: 4   YTNILVEQRGRVGLVTLNRPEALNALDKATMDQLVAAVTAMDADPGVGAVVIT-GSSKAF 62

Query: 62  CDGVDVADHVPEKVDEMI--DLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDIVI 119
             G D+ +   +   +M   D F G + +   + +  +  V+G +LGGGCEL   CD +I
Sbjct: 63  AAGADIKEMASQGYMDMYAADWFRG-WEDFTRLRIPVIAAVSGFALGGGCELAMMCDFII 121

Query: 120 ASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVL 178
           A + AK GQPEINL V P +  +    + +G  KAM++ILTG+ I A+EAE  GLV+ V+
Sbjct: 122 AGDNAKFGQPEINLGVLPGMGGSQRLTRAVGKAKAMDMILTGRFIGAEEAERSGLVSRVV 181

Query: 179 PVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATEDA 238
           P E   E A K      SKS+PVAM A+ A+ A       Q +     I+     A+ED 
Sbjct: 182 PAENVVEEALKAAEVIASKSKPVAMLAKEAVNAAFETGLAQGVLFERRIF-HSLFASEDQ 240

Query: 239 NEGLASFLEKRKPVF 253
            EG+A+F EKR+P F
Sbjct: 241 KEGMAAFTEKRQPEF 255


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: 177
Number of extensions: 10
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: 256
Length of database: 258
Length adjustment: 24
Effective length of query: 232
Effective length of database: 234
Effective search space:    54288
Effective search space used:    54288
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