GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudomonas fluorescens FW300-N2E2

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate Pf6N2E2_1147 Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)

Query= metacyc::MONOMER-18320
         (256 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1147
          Length = 257

 Score =  149 bits (376), Expect = 6e-41
 Identities = 92/260 (35%), Positives = 139/260 (53%), Gaps = 7/260 (2%)

Query: 1   MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59
           M + TIL E KD+V  ITLN P + N L   ++ E+N+AL  ++ DP I  +V      K
Sbjct: 1   MSYETILLEIKDRVGLITLNRPQALNALNAQIVSELNQALDSLEADPKIGCIVLT-GSKK 59

Query: 60  AFCDGVDVADHVPEKVDEMI--DLFHGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDI 117
           AF  G D+ +       ++   DLF    R +A      +  VNG +LGGGCEL   CD 
Sbjct: 60  AFAAGADIKEMAELTYPQIYLDDLFSDSDR-VANRRKPIIAAVNGFALGGGCELALMCDF 118

Query: 118 VIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNV 176
           ++A + AK GQPE+NL V P +       + +G  KAME+ LTG+ I A EAE  G+V  
Sbjct: 119 ILAGDNAKFGQPEVNLGVLPGMGGTQRLTRAVGKAKAMEMCLTGRFIDAVEAERCGIVAR 178

Query: 177 VLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQGCMATE 236
           ++P +   + A K  A   SKS P++M  + ++     +   + ++    ++     AT+
Sbjct: 179 IVPADELLDDALKTAALIASKSVPISMMVKESVNRAFEVSLSEGVRFERRVF-HAAFATQ 237

Query: 237 DANEGLASFLEKRKPVFKDK 256
           D  EG+A+F+ KR   F+DK
Sbjct: 238 DQKEGMAAFVAKRAAEFQDK 257


Lambda     K      H
   0.322    0.136    0.401 

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: 164
Number of extensions: 12
Number of successful extensions: 5
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: 256
Length of database: 257
Length adjustment: 24
Effective length of query: 232
Effective length of database: 233
Effective search space:    54056
Effective search space used:    54056
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 (21.9 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