GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Brevibacterium jeotgali SJ5-8

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_101588405.1 BJEO58_RS05430 crotonase/enoyl-CoA hydratase family protein

Query= metacyc::MONOMER-13469
         (259 letters)



>NCBI__GCF_900169175.1:WP_101588405.1
          Length = 302

 Score =  161 bits (408), Expect = 1e-44
 Identities = 101/263 (38%), Positives = 150/263 (57%), Gaps = 16/263 (6%)

Query: 6   IILEKDGNVASITLNRPKALNALN-----AATLKEIDAAINDIAEDDNVYAVIITGSGKA 60
           +++E+DG+V + TLNRP + N ++     AA +  +DAA  D A    V  VI+TG+GKA
Sbjct: 41  LLVERDGHVETWTLNRPDSRNPISDDDMVAAIIDAVDAANADPA----VRVVILTGAGKA 96

Query: 61  FVAGADIAEMKDLTAV-EGRKFSVLGN------KIFRKLENLEKPVIAAINGFALGGGCE 113
           F AG D+ +M+D + +  G    + G       +I   L+ L+ P+IAA+NG A+G GC+
Sbjct: 97  FSAGGDVKKMRDRSGMFGGHPHQMRGGYRYGIQQIPLALQRLDAPLIAAVNGPAVGAGCD 156

Query: 114 LSLSCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEAL 173
           L+   D+RIAS  A F +  V LGI PG GG   L R +G   A E+  TG  ++A+ AL
Sbjct: 157 LTAMADMRIASETAWFAESFVKLGIIPGDGGAWFLPRLVGPARAAEMTLTGDRVDAKTAL 216

Query: 174 RIGLVNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFG 233
             GLV++VV P+ L+ EA+AL D + VN P AVRM K  + +     + + +   A +  
Sbjct: 217 EWGLVSRVVAPEDLMTEARALADRVAVNPPHAVRMAKKLLKESDGSSLSSLLELSAAMQP 276

Query: 234 ECFATEDRVEGMTAFVEKRDKAF 256
                 D  E + AF++KRD  F
Sbjct: 277 LAHHAPDHAEAIDAFLDKRDPTF 299


Lambda     K      H
   0.318    0.136    0.376 

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: 205
Number of extensions: 16
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: 259
Length of database: 302
Length adjustment: 26
Effective length of query: 233
Effective length of database: 276
Effective search space:    64308
Effective search space used:    64308
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