GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Rhizobium etli CFN 42

Align BadI (characterized)
to candidate WP_011423740.1 RHE_RS01800 enoyl-CoA hydratase

Query= metacyc::MONOMER-892
         (260 letters)



>NCBI__GCF_000092045.1:WP_011423740.1
          Length = 257

 Score =  117 bits (294), Expect = 2e-31
 Identities = 89/270 (32%), Positives = 132/270 (48%), Gaps = 29/270 (10%)

Query: 1   MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGY-DKDVGAIVLAGAGD 59
           M +E LI E R  V  + +NRP  +NA   T   EL KA Y A + D+ +GAIV+ G+ +
Sbjct: 1   MAYETLIVETRGNVGLVTLNRPQALNALNSTVLKEL-KAAYAAFHADEAIGAIVITGS-E 58

Query: 60  RAFCTGGDQSTHDGNYDGRGTVGLPMEELHTA--------IRDVPKPVIARVQGYAIGGG 111
           RAF  G D               L   +++ +        I    KPVIA V G+A+GGG
Sbjct: 59  RAFAAGADIKEMQS---------LQFADIYKSDFISGWDDIAKARKPVIAAVSGFALGGG 109

Query: 112 NVLATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKE 171
             LA +CD  I SE A FGQ    +G +    G+  L R VG+ KA ++    +     E
Sbjct: 110 CELAMMCDFIIASETAKFGQPEITLGVIPGMGGSQRLTRAVGKAKAMDLVLTGRMMDAAE 169

Query: 172 AEAMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFN--MDTAHQAGIAGMGMY 229
           AE  GL +  V  + L  E     E++   S  ++ +AK + N   +T  + G+     +
Sbjct: 170 AERSGLVSRVVAPERLLDEALAAAEKIASLSQPSVMMAKEAVNRAFETTLEEGL----RF 225

Query: 230 ALKLYYD---TDESREGVKALQEKRKPEFR 256
             +L++    TD+ +EG+ A  EKRKP F+
Sbjct: 226 ERRLFHSLFATDDQKEGMAAFVEKRKPAFK 255


Lambda     K      H
   0.319    0.138    0.418 

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: 152
Number of extensions: 12
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: 260
Length of database: 257
Length adjustment: 24
Effective length of query: 236
Effective length of database: 233
Effective search space:    54988
Effective search space used:    54988
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 (21.7 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