GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dgoK in Pseudomonas simiae WCS417

Align 2-keto-3-deoxygalactonate kinase protein; EC 2.7.1.58 (characterized, see rationale)
to candidate GFF30 PS417_00155 2-dehydro-3-deoxygalactonokinase

Query= uniprot:D8J0Z3
         (319 letters)



>lcl|FitnessBrowser__WCS417:GFF30 PS417_00155
           2-dehydro-3-deoxygalactonokinase
          Length = 319

 Score =  315 bits (806), Expect = 1e-90
 Identities = 172/311 (55%), Positives = 209/311 (67%), Gaps = 6/311 (1%)

Query: 10  LIALDWGTSSLRCYRYDGSGQVVERRAHPWGIMNLPAVEH---GDDAQAPYRAALEAACG 66
           LIALDWGTSSLR Y+   +G V+E+RA  WGIM+LP+      G      +  A +AACG
Sbjct: 5   LIALDWGTSSLRAYKLGLAGVVLEQRALAWGIMHLPSEPRDIAGVRCGNGFELAFDAACG 64

Query: 67  DWIAAAPEAALIAAGMVGSKQGWREAAYLTVPLAPDGIGRKLTEVDTGLGRSLWIIPGLL 126
           DW+ A P   +IA GMVGS QGW EAAY   P+    +G+ L +V +  G  + I+PG++
Sbjct: 65  DWLDAEPGLPVIACGMVGSAQGWSEAAYRPTPVDVASLGQALHKVRSLRGVDVHIVPGVI 124

Query: 127 QNSALPNVMRGEETQVIGALQQQRQSELLIGLPGTHSKWVRVVEGRIEHFDTFMTGEVYG 186
           +   LPNVMRGEETQV+G LQ    +++LIGLPG+HSKWV VVEGRI HFDTFMTGEV+ 
Sbjct: 125 EQVGLPNVMRGEETQVLGVLQGLG-ADMLIGLPGSHSKWVEVVEGRITHFDTFMTGEVFA 183

Query: 187 ALCGHTILGRTMHKPDVPDDAAFVRGARVAQGPQGQAGVLSNIFSSRTLGLTGELAPEAQ 246
            L  H+ILGRT    +     AF RG  VA+   GQ GVLS +FS+RTLGLTGELAP+ Q
Sbjct: 184 VLSKHSILGRTQQPSERFQAEAFDRGVHVARSNDGQRGVLSTLFSARTLGLTGELAPDQQ 243

Query: 247 PDYLSGLLIGHEIAALKSLYPAQQAPIVLIGDAGLCRRYRLALELYGLGPVSEADAATEA 306
           PDYLSGLLIGHE+A L     A+  PI+L+G A LC RY+ AL L G   VS A  A E 
Sbjct: 244 PDYLSGLLIGHELAGLPD--SAKHKPIILVGAAPLCARYQRALALCGFAHVSLAQEAAER 301

Query: 307 GLWILARHAGL 317
           GLW LA  AGL
Sbjct: 302 GLWQLAVAAGL 312


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: 411
Number of extensions: 22
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: 319
Length adjustment: 28
Effective length of query: 291
Effective length of database: 291
Effective search space:    84681
Effective search space used:    84681
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: 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 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