GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudarthrobacter sulfonivorans Ar51

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_083510176.1 AU252_RS00745 enoyl-CoA hydratase-related protein

Query= BRENDA::D3RXI0
         (252 letters)



>NCBI__GCF_001484605.1:WP_083510176.1
          Length = 279

 Score =  108 bits (271), Expect = 9e-29
 Identities = 80/259 (30%), Positives = 135/259 (52%), Gaps = 15/259 (5%)

Query: 6   IKVEKDERVARIKIANPPV-NVLDMETMKEIISAIDEVE---GVDVIVFSGEG-KSFSAG 60
           +  E+   V  + I  P   N ++ + ++ +  A++  E   G+  +V +G G K+F AG
Sbjct: 22  VTAEEIGHVFLVTINRPEARNAVNPDVIRGVGRALEHAEECPGIRAVVITGSGDKAFCAG 81

Query: 61  AEIKEH----FPDKAPEMIRW-FTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVL 115
           A++K      F +    M +W F   +   +     T+AA+ GFALGGG E+ +A D  +
Sbjct: 82  ADLKSAAVGAFGEIPEGMEQWGFAGFVKHHI--SKPTIAAINGFALGGGTEIVLASDLAI 139

Query: 116 ASKNAKLGVPEITLAHYPPVAIAL-LPRMIGWKNAYELILTGEAITAERAFEIGLVNKVF 174
           AS  A  G+PE+ L  +     A    + +  K A E++LTG+ + A+RA EIGLVN+V 
Sbjct: 140 ASSEAVFGLPEVKLGIFAGAGGAFRAGQQVPKKIAMEMLLTGQPLPAQRALEIGLVNRVV 199

Query: 175 EDENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLS-LFDVINDVYLSQ-LVKSE 232
             E    +  +    + E + +A++ TK+     T+    S   D     + +Q L++S 
Sbjct: 200 PPEEVLPAALELARQICENAPLAVQTTKRIANGITDGTVESDQADWARSEWEAQKLMRST 259

Query: 233 DAVEGLKAFLEKRKPEWKG 251
           D +EG++AF EKR P+W+G
Sbjct: 260 DFMEGMRAFAEKRAPQWQG 278


Lambda     K      H
   0.318    0.136    0.382 

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: 173
Number of extensions: 12
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: 252
Length of database: 279
Length adjustment: 25
Effective length of query: 227
Effective length of database: 254
Effective search space:    57658
Effective search space used:    57658
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 (21.7 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