GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Putida:PP_4030 PP_4030 Enoyl-CoA
           hydratase/isomerase family protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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