GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Cupriavidus basilensis 4G11

Align BadI (characterized)
to candidate RR42_RS18250 RR42_RS18250 enoyl-CoA hydratase

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



>FitnessBrowser__Cup4G11:RR42_RS18250
          Length = 258

 Score =  120 bits (301), Expect = 3e-32
 Identities = 84/268 (31%), Positives = 131/268 (48%), Gaps = 24/268 (8%)

Query: 1   MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60
           M +E+++ E R  V  + +NRP  +NA      DEL  AL     D+ +G+IV+ G+ +R
Sbjct: 1   MPYENILVETRGRVGLVTLNRPKALNALNDALMDELGVALLAFDADEAIGSIVITGS-ER 59

Query: 61  AFCTGGD---------QSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGG 111
           AF  G D            + G+Y  R             IR + KPVIA V GYA+GGG
Sbjct: 60  AFAAGADIGMMAKYSYMDVYKGDYITRNW---------ETIRRIRKPVIAAVAGYALGGG 110

Query: 112 NVLATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKE 171
             LA +CD+ I ++ A FGQ   K+G++    GT  L R V + KA ++    +     E
Sbjct: 111 CELAMMCDIIIAADTARFGQPEVKLGTMPGAGGTQRLPRAVSKAKAMDLCLTSRMMDAAE 170

Query: 172 AEAMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYAL 231
           AE  GL +  V  D+L  +     E +   S   + + K S N   A++  ++       
Sbjct: 171 AERAGLVSRVVAADKLLDDALAAAETIAGFSLPVVMMIKESIN--AAYETSLSEGVHLER 228

Query: 232 KLYYD---TDESREGVKALQEKRKPEFR 256
           +L++    T++ +EG+ A  EKR P+F+
Sbjct: 229 RLFHSTFATEDQKEGMAAFVEKRAPDFK 256


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: 176
Number of extensions: 16
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: 260
Length of database: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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 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