GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Pseudomonas putida KT2440

Align BadK (characterized)
to candidate PP_4030 PP_4030 Enoyl-CoA hydratase/isomerase family protein

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__Putida:PP_4030
          Length = 280

 Score =  126 bits (316), Expect = 6e-34
 Identities = 86/260 (33%), Positives = 131/260 (50%), Gaps = 12/260 (4%)

Query: 9   ETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADI- 67
           E    V  + +NRP+ +NA+N A  + +       D  D +  +VI+G  + F+AG D+ 
Sbjct: 20  ELTDSVAHVQINRPEKVNAMNAAFWEEIVDIFQWIDDTDAVRVVVISGAGKHFSAGIDLM 79

Query: 68  --ASMAAWSYSDV-YGSNFITR-------NWETIRQIRKPVLAAVAGLAYGGGCELALAC 117
             AS+A     DV   + F+ +       ++  +   RKPVLAAV G   GG  +L  AC
Sbjct: 80  MLASLAGQMGKDVGRNARFLRKTIQRLQASFTAVDACRKPVLAAVQGYCIGGAIDLISAC 139

Query: 118 DIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLV 177
           D+    R A+F++ EI +G+    G  QRLPR IG     ++  + R + A+EA R GLV
Sbjct: 140 DMRYCSRDAQFSIKEIDMGMAADVGTLQRLPRIIGDGIMRELAFTGRNVEADEALRIGLV 199

Query: 178 SRVVDDD-RLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFA 236
           +RV DD   L D   A+A  IAA S  A+   KE L+   +  + +G+ +      A   
Sbjct: 200 NRVYDDQAALMDGVFAIAREIAAKSPIAVAGTKEMLSYMRDHRIDDGLDYIATWNAAMLQ 259

Query: 237 SADAREGIQAFLEKRAPCFS 256
           S D R  + A + K+ P F+
Sbjct: 260 SEDLRVAVAAHMSKQKPTFA 279


Lambda     K      H
   0.321    0.135    0.389 

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: 125
Number of extensions: 6
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: 258
Length of database: 280
Length adjustment: 25
Effective length of query: 233
Effective length of database: 255
Effective search space:    59415
Effective search space used:    59415
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