GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Herbaspirillum seropedicae SmR1

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate HSERO_RS12745 HSERO_RS12745 enoyl-CoA hydratase

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__HerbieS:HSERO_RS12745
          Length = 260

 Score =  120 bits (300), Expect = 4e-32
 Identities = 77/259 (29%), Positives = 134/259 (51%), Gaps = 11/259 (4%)

Query: 3   YKKIKVEKDERVARIKIANPPVNVLDMETMKEIISAIDEVEG---VDVIVFSGEG-KSFS 58
           Y  +K+EK    A + ++NPP N      + ++   + E+     +  +V +GEG K FS
Sbjct: 4   YTNLKLEKTGHTAVLTLSNPPANTWTRAALADLTRLVKELNADRDIYTLVVTGEGEKFFS 63

Query: 59  AGAEIKEHFPD----KAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFV 114
           AGA++K  F D     A EM R F +  + +   + +++AA+ G+A+GGG E A+ACD  
Sbjct: 64  AGADLKL-FADGDKAMAREMARRFGEAFETLSAFRGVSIAAINGYAMGGGLECALACDIR 122

Query: 115 LASKNAKLGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKV 173
           +A + A++ +PE  +   P       LP ++G   A  +IL GE + AE A  IGLV +V
Sbjct: 123 IAEEQAQMALPEAAVGLLPCAGGTQNLPWLVGEGWAKRMILCGERVNAETALRIGLVEEV 182

Query: 174 FEDENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSED 233
                  E          ++S  ++  +K+ +  +      ++     ++++  L  ++D
Sbjct: 183 VPRGQARERALALAQQAEKQSPSSVAASKQLIQGARHNPLGTILQTERELFV-DLFDTQD 241

Query: 234 AVEGLKAFLEKRKPEWKGR 252
             EG++AFLEKR P+WK +
Sbjct: 242 QREGVQAFLEKRSPQWKNQ 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: 145
Number of extensions: 8
Number of successful extensions: 4
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 17 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