GapMind for catabolism of small carbon sources

 

Aligments for a candidate for garK in Pseudomonas fluorescens FW300-N2C3

Align glycerate 2-kinase (EC 2.7.1.165) (characterized)
to candidate AO356_22870 AO356_22870 glycerate kinase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22870 AO356_22870
           glycerate kinase
          Length = 378

 Score =  595 bits (1533), Expect = e-175
 Identities = 296/376 (78%), Positives = 328/376 (87%)

Query: 1   MKIIIAPDSFKDSLSAEGVAQAIAAGLSEVWPQAQLIQCPMADGGEGTVDAVLAACKGEL 60
           MKIIIAPDSFKDSLSA+GVA AIA GL++VWP AQLI+CPMADGGEGTV++VLAAC G+ 
Sbjct: 1   MKIIIAPDSFKDSLSAQGVADAIAQGLAQVWPDAQLIKCPMADGGEGTVESVLAACNGQW 60

Query: 61  RRQQVRGPLGGTVEARWGWLADSHTAIIEMAEASGLQLVPPGQRDACTSTTYGTGELIRA 120
           R  +VRGPLG  VEARWGWLA+S TAIIEMAEASGLQLV PGQRDAC S+TYGTGELIRA
Sbjct: 61  RHTRVRGPLGVVVEARWGWLAESRTAIIEMAEASGLQLVAPGQRDACASSTYGTGELIRA 120

Query: 121 ALDLGAERIILAIGGSATNDAGAGAMQALGAQLFDAEAQTLPPGGLALSRLAHISLENLD 180
           ALD GAER+ILAIGGSATNDAGAGA+QALG  L D + Q LPPGGLAL+ LA I L  LD
Sbjct: 121 ALDEGAERVILAIGGSATNDAGAGALQALGVALLDDQGQPLPPGGLALANLARIDLSELD 180

Query: 181 PRLAQVRFEIAADVNNPLCGPHGASAIFGPQKGASPVHVQQLDAALGHFADHCARVLPKD 240
           PRLA V FEIAADV+NPLCGPHGASA+FGPQKGAS   VQ LD ALGHFA+ CA+ L KD
Sbjct: 181 PRLAHVSFEIAADVDNPLCGPHGASAVFGPQKGASASQVQALDRALGHFAEQCAQALNKD 240

Query: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRAGVEVVAELVGLEDAVRGADLVITGEGRFDAQTL 300
           VRDEPGSGAAGGLGFAAKAFLGAQFR GV+VVA+L GL DA+ GADLVITGEGRFDAQTL
Sbjct: 241 VRDEPGSGAAGGLGFAAKAFLGAQFRTGVDVVAQLTGLADAIEGADLVITGEGRFDAQTL 300

Query: 301 RGKTPFGVARIAGQHNVPVIVIAGTLGEGYEQMYAHGVAAAFALPAGPMSLEQACSEAPR 360
           RGKTPFGVARIA Q  VPV+VIAGTLGEGY+ +Y HG+ AAFAL +GPM+L++AC +APR
Sbjct: 301 RGKTPFGVARIARQQGVPVLVIAGTLGEGYQALYEHGIDAAFALASGPMTLQEACVDAPR 360

Query: 361 LLRERASDIARVWRLA 376
           LL ERA DIAR+WR+A
Sbjct: 361 LLSERAQDIARLWRVA 376


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: 519
Number of extensions: 14
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: 378
Length adjustment: 30
Effective length of query: 350
Effective length of database: 348
Effective search space:   121800
Effective search space used:   121800
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 paper from 2022 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