GapMind for catabolism of small carbon sources

 

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

Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate Ac3H11_700 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)

Query= metacyc::MONOMER-12748
         (320 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_700
          Length = 319

 Score =  141 bits (355), Expect = 2e-38
 Identities = 113/313 (36%), Positives = 152/313 (48%), Gaps = 17/313 (5%)

Query: 5   DILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSLG 64
           D+++ GE +  F     G+   +Q F     G  SN  I  AR G + A+L+R+G+D+ G
Sbjct: 10  DVVALGEALVEFNQTRPGEPQYLQGF----GGDTSNAVIAAARAGARTAYLTRLGSDAFG 65

Query: 65  RFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDL-- 122
           + +LD    EG+D   V  D  HPTG    +    G +    Y R GSAAS +A + L  
Sbjct: 66  QALLDLWAREGVDTTAVERDAQHPTGIYFVTHGAAGHE--FSYLRAGSAASRMAPAWLAD 123

Query: 123 ----DPA--LLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPS 176
                PA  L + R LH +GI  A+S SA + +   M   R+AG  V+FDPNLR  LWP 
Sbjct: 124 ESVKGPAAVLQQCRILHVSGISLAVSASACDTAYEAMRVARAAGARVAFDPNLRLKLWPL 183

Query: 177 EALMIREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYY 236
            A     I    +L    LPGL +   L G  D   IA +   QGA  VV+KLGA G   
Sbjct: 184 -ARARACIAHAVSLCDIFLPGLDDMAALLGLSDADAIADWGHAQGAATVVVKLGADGVLL 242

Query: 237 RTQLDAGFVEGVPVAQV--VDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQS 294
            +   A   + VP   V  VD  GAGD F   L++ L     +  AV+ AN   S AVQ 
Sbjct: 243 SSADPAVPRQRVPGRSVALVDATGAGDCFDGNLLARLALGDDLAAAVRYANTAASLAVQG 302

Query: 295 RGDMEGLPLRHEL 307
            G +  LP   ++
Sbjct: 303 FGAVAPLPTAQQV 315


Lambda     K      H
   0.321    0.138    0.414 

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: 295
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: 320
Length of database: 319
Length adjustment: 28
Effective length of query: 292
Effective length of database: 291
Effective search space:    84972
Effective search space used:    84972
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.

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