GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Pseudomonas putida KT2440

Align BadI (characterized)
to candidate PP_2217 PP_2217 enoyl-CoA hydratase

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



>FitnessBrowser__Putida:PP_2217
          Length = 257

 Score =  105 bits (262), Expect = 9e-28
 Identities = 78/260 (30%), Positives = 125/260 (48%), Gaps = 9/260 (3%)

Query: 1   MQFEDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60
           M FE ++ +I   V  I +NRP  +NA       E+ +AL +   D ++G +VL G+  +
Sbjct: 1   MAFETILLDIHGKVGLITLNRPQALNALNAQIVGEINQALDQLERDPNIGCVVLTGSA-K 59

Query: 61  AFCTGGD-QSTHDGNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICD 119
           AF  G D +   +  Y       L  +    A R   KP+IA V G+A+GGG  LA +CD
Sbjct: 60  AFAAGADIKEMAELQYPQIYVDDLFSDADRIANRR--KPIIAAVSGFALGGGCELAMMCD 117

Query: 120 LTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLAN 179
             + ++ A FGQ    +G +    GT  L R VG+ KA E+    +    +EAE  GL  
Sbjct: 118 FILAADNAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMELCLTGRLMGAEEAERAGLVA 177

Query: 180 LCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKLY---YD 236
             VP  EL  E  K    +  +S     + K S N   A +  ++    +  +++   + 
Sbjct: 178 RIVPQAELVEEALKVAATIASKSIPVSMMVKESVN--RAFEVTLSEGVRFERRVFHAAFS 235

Query: 237 TDESREGVKALQEKRKPEFR 256
           T++ +EG+ A   KR+ +F+
Sbjct: 236 TEDQKEGMAAFIAKREAQFK 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: 145
Number of extensions: 8
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: 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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