GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas stutzeri RCH2

Align crotonase (EC 4.2.1.150) (characterized)
to candidate GFF2604 Psest_2654 fatty oxidation complex, alpha subunit FadB

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



>FitnessBrowser__psRCH2:GFF2604
          Length = 715

 Score =  136 bits (343), Expect = 1e-36
 Identities = 80/180 (44%), Positives = 106/180 (58%), Gaps = 3/180 (1%)

Query: 23  KALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEMKDLTAVEGRKF- 81
           +++N  N  TL ++  A++ I  D +V  VI+T     F+ GADI E  D   +   +  
Sbjct: 27  ESVNKFNRLTLNDLRQAVDAIKADASVKGVIVTSGKDVFIVGADITEFVDNFKMADEELV 86

Query: 82  --SVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKFGQPEVGLGIT 139
             ++  NKIF   E+L  P +AAING ALGGG E+ ++ D R+ S+ AK G PEV LGI 
Sbjct: 87  AGNLEANKIFSDFEDLGVPTVAAINGIALGGGFEMCMAADYRVMSTTAKVGLPEVKLGIY 146

Query: 140 PGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLEEAKALVDAII 199
           PGFGGT RL R IGV  A E I +GK   AE+AL++  V+ VV PDKL   A  LV   I
Sbjct: 147 PGFGGTVRLPRLIGVDNAVEWIASGKENRAEDALKVHAVDAVVAPDKLQAAALDLVKRAI 206


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: 399
Number of extensions: 22
Number of successful extensions: 2
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: 715
Length adjustment: 32
Effective length of query: 227
Effective length of database: 683
Effective search space:   155041
Effective search space used:   155041
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: 51 (24.3 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