GapMind for catabolism of small carbon sources

 

Aligments for a candidate for garK in Pseudomonas fluorescens FW300-N2E3

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate AO353_26900 AO353_26900 glycerate kinase

Query= metacyc::MONOMER-20837
         (380 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_26900 AO353_26900 glycerate
           kinase
          Length = 380

 Score =  605 bits (1559), Expect = e-178
 Identities = 305/379 (80%), Positives = 335/379 (88%)

Query: 1   MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60
           MKI+IAPDSFKDSLSAE VA AIA GL+EVWP A L++CPMADGGEGTV+++LAAC+GEL
Sbjct: 1   MKIVIAPDSFKDSLSAEAVATAIALGLAEVWPDATLVKCPMADGGEGTVESILAACEGEL 60

Query: 61  RRQQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRA 120
           R   V+GPLG  V+A WGWL  +HTAIIEMAEASGLQLVP GQRDAC S+T+GTGELIRA
Sbjct: 61  RSASVQGPLGIQVDAHWGWLPHNHTAIIEMAEASGLQLVPVGQRDACISSTFGTGELIRA 120

Query: 121 ALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLD 180
           ALD GA+RIILAIGGSATNDAGAGA+QALG +L DA+ QTL PGGLAL++LA I L  +D
Sbjct: 121 ALDAGAQRIILAIGGSATNDAGAGALQALGVRLLDAQGQTLQPGGLALAQLARIDLSEMD 180

Query: 181 PRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKD 240
           PRLA VRFEIAADVNNPLCGPHGASAIFGPQKGAS   VQQLD ALGHFA  CA+ L KD
Sbjct: 181 PRLASVRFEIAADVNNPLCGPHGASAIFGPQKGASVEQVQQLDQALGHFAGICAQTLGKD 240

Query: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTL 300
           +RDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVA+LVGLE+AVR ADLVITGEGRFDAQTL
Sbjct: 241 LRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVADLVGLEEAVRDADLVITGEGRFDAQTL 300

Query: 301 RGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPR 360
           RGKTPFGVARIA Q  VPVIVIAGTLGEGY+QMY HGV AAFAL +GPM+LEQAC++APR
Sbjct: 301 RGKTPFGVARIARQQGVPVIVIAGTLGEGYQQMYEHGVDAAFALASGPMTLEQACTDAPR 360

Query: 361 LLRERASDIARVWRLASSK 379
           LL +RA DIARVWRLA  K
Sbjct: 361 LLHDRARDIARVWRLAVHK 379


Lambda     K      H
   0.318    0.135    0.398 

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: 531
Number of extensions: 7
Number of successful extensions: 1
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: 380
Length of database: 380
Length adjustment: 30
Effective length of query: 350
Effective length of database: 350
Effective search space:   122500
Effective search space used:   122500
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: 50 (23.9 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 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