GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Acidovorax sp. GW101-3H11

Align 2-keto-3-deoxygalactonate kinase protein; EC 2.7.1.58 (characterized, see rationale)
to candidate Ac3H11_602 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58)

Query= uniprot:D8J0Z3
         (319 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_602
          Length = 349

 Score =  325 bits (834), Expect = 8e-94
 Identities = 175/321 (54%), Positives = 208/321 (64%), Gaps = 9/321 (2%)

Query: 7   DCALIALDWGTSSLRCYRYDGSGQVVERRAHPWGIMNLP---AVEHGDDAQAPYRAALEA 63
           +  LIALDWGTS+LR +R    G+V+E R  PWGIMNLP   A     +  A +  AL+ 
Sbjct: 11  EAGLIALDWGTSALRAFRMGAHGEVLETRHRPWGIMNLPPTTASAADIEPGAAFERALQD 70

Query: 64  ACGDWIAAAPEAALIAAGMVGSKQGWREAAYLTVPLAPDGIGRKLTEVDTGLGRSLWIIP 123
            CGDW+AA P   L+A GMVGS QGWREA YL  P + D + R LT  +   G  L I+P
Sbjct: 71  TCGDWLAATPGLPLLACGMVGSAQGWREAKYLPTPTSLDALARGLTLAERRDGPPLHIVP 130

Query: 124 GLLQNSALPNVMRGEETQVIGALQQ---QRQSELLIGLPGTHSKWVRVVEGRIEHFDTFM 180
           GLLQ   LPNVMRGEETQV+G L     +    +LIGLPGTHSKWV   +G IE F TFM
Sbjct: 131 GLLQQGTLPNVMRGEETQVLGVLAGLALRADGPVLIGLPGTHSKWVLARQGHIEQFHTFM 190

Query: 181 TGEVYGALCGHTILGRTMHKPDVPDDAAFVRGARVAQGPQGQAGVLSNIFSSRTLGLTGE 240
           TGEV+ AL GHTILG+TM     PDD AF RG  VA+G     G+LS+IFS+RTLGLTG 
Sbjct: 191 TGEVFAALRGHTILGKTMQAAVTPDDDAFARGLEVARGSDAALGLLSHIFSTRTLGLTGA 250

Query: 241 LAPEAQPDYLSGLLIGHEIAAL---KSLYPAQQAPIVLIGDAGLCRRYRLALELYGLGPV 297
           LAP AQ DYLSGLLIGHE+A+L   +   P     +VL G+  LCRRY +AL+ YG    
Sbjct: 251 LAPTAQADYLSGLLIGHEVASLSRAQDQTPTTPQTLVLCGEPDLCRRYAIALQTYGFAAP 310

Query: 298 SEADAATEAGLWILARHAGLV 318
           + A  AT  GLW +A  AGLV
Sbjct: 311 TIATQATATGLWQIALAAGLV 331


Lambda     K      H
   0.320    0.137    0.423 

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: 396
Number of extensions: 13
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: 319
Length of database: 349
Length adjustment: 28
Effective length of query: 291
Effective length of database: 321
Effective search space:    93411
Effective search space used:    93411
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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