GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Pseudomonas fluorescens FW300-N2C3

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate AO356_05215 AO356_05215 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05215
          Length = 318

 Score =  207 bits (526), Expect = 4e-58
 Identities = 125/318 (39%), Positives = 171/318 (53%), Gaps = 7/318 (2%)

Query: 3   KYALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVE---VKDG 59
           K ALVGD+GGTNAR AL       +   +  +  DY   E  I+VYL    ++   +   
Sbjct: 2   KLALVGDIGGTNARFALWK--DHTLENIQVLATADYACPEDAIQVYLGGLGLKPGAIGSV 59

Query: 60  CIAIACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQF 119
           C+++A P++GD    TN+ W  S     K L    L ++NDF+A+++ +  L+ +     
Sbjct: 60  CLSVAGPVSGDEFRFTNNHWRLSNLAFCKTLQVEKLLLVNDFSAMALGMTCLRPDEYRVV 119

Query: 120 GGAEPVEGKPIAVYGAGTGLGVAHLVHVDK-RWVSLPGEGGHVDFAPNSEEEAIILEILR 178
               P   +P  V G GTGLGV  L+ + + R+ +LPGEGGHVD   +S  E  + + + 
Sbjct: 120 CEGTPEPMRPAVVIGPGTGLGVGTLLDLGEGRFAALPGEGGHVDLPMSSPRETQLWQHIY 179

Query: 179 AEIGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFC 238
            EIGHVSAE  LSG GL  +YRAI   D  +P    P+ IT   LA         L  FC
Sbjct: 180 NEIGHVSAETALSGSGLPRVYRAICAVDGHVPVLDTPESITAAGLAGDPI-ALEVLEQFC 238

Query: 239 VIMGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYL 298
             +GR  GN  L LG  GGV+I GG+VPRF +FF  SGF   F DKG   +Y   IPV+L
Sbjct: 239 RWLGRVAGNNVLTLGGRGGVYIVGGVVPRFADFFLESGFARCFADKGCMSDYFKGIPVWL 298

Query: 299 IVHDNPGLLGSGAHLRQT 316
           +     GL+G+G  L Q+
Sbjct: 299 VTAPYSGLMGAGVALEQS 316


Lambda     K      H
   0.322    0.141    0.426 

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: 356
Number of extensions: 19
Number of successful extensions: 4
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: 321
Length of database: 318
Length adjustment: 28
Effective length of query: 293
Effective length of database: 290
Effective search space:    84970
Effective search space used:    84970
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: 48 (23.1 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