GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Bacillus altitudinis 41KF2b

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase

Query= BRENDA::D3RXI0
         (252 letters)



>NCBI__GCF_000691145.1:WP_035704417.1
          Length = 260

 Score =  119 bits (299), Expect = 5e-32
 Identities = 79/252 (31%), Positives = 129/252 (51%), Gaps = 10/252 (3%)

Query: 10  KDERVARIKIANPP-VNVLDMETMKEIISAIDEVE---GVDVIVFSGEG-KSFSAGAEIK 64
           +D+ +  + +  P   N L    ++EI   I E++    +  ++ +G G K F AGA++K
Sbjct: 10  QDDYIGIMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLK 69

Query: 65  EH---FPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAK 121
           E       +A E +    Q    +       +A + G ALGGG ELA+ACD  +A   A 
Sbjct: 70  ERRLMTEQEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAA 129

Query: 122 LGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFE 180
           LG+PE  LA  P       LPR+IG   A E+I TG ++ AE A +IGL+ ++   ++  
Sbjct: 130 LGLPETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSLM 189

Query: 181 ESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKA 240
                    + +   +AL+  K+A+  S + +  +      + YL +L+ +ED +EGLKA
Sbjct: 190 NDAITLAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYL-RLIHTEDRLEGLKA 248

Query: 241 FLEKRKPEWKGR 252
           F EKR P ++G+
Sbjct: 249 FQEKRTPHYRGK 260


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: 147
Number of extensions: 9
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: 260
Length adjustment: 24
Effective length of query: 228
Effective length of database: 236
Effective search space:    53808
Effective search space used:    53808
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 Sep 24 2021. 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