GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Sphingomonas koreensis DSMZ 15582

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Ga0059261_2669 Ga0059261_2669 Lactate dehydrogenase and related dehydrogenases

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>FitnessBrowser__Korea:Ga0059261_2669
          Length = 318

 Score =  179 bits (453), Expect = 1e-49
 Identities = 117/279 (41%), Positives = 151/279 (54%), Gaps = 16/279 (5%)

Query: 31  QHDAFVAALKDADGGIGSSVKIT-PAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLA 89
           +HDA    + D         +IT   +L    R + +     GF+  D+      GI + 
Sbjct: 46  EHDALCPTVTD---------RITRDVILTEGRRARIIGNYGAGFEHIDLDAAREAGIAVT 96

Query: 90  NTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGL 149
           NTPDVLT++TAD   +LIL + RR  E    ++AG W       L G  ++GK LG+VG 
Sbjct: 97  NTPDVLTDATADIAMTLILMATRRAGEGERELRAGEWTGWRPTHLLGRSLRGKVLGLVGY 156

Query: 150 GRIGGAVARRAALGFNMKVLYTNRS-ANPQAEEAYGARRVELAELLATADFVCLQVPLTP 208
           GRI  AVA RA   F MK+   +RS A    E  Y A    L  LL+ AD V L  P   
Sbjct: 157 GRIARAVADRAK-AFGMKIAVHSRSRAEDVPETDYHA---SLQSLLSIADVVSLHAPGGA 212

Query: 209 ETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDS 268
            T+H+I AA L +MK+ A+L+N  RG  +DE AL EAL+ GTI  AGLDV+E EP   ++
Sbjct: 213 ATRHMIDAAALSAMKRDAVLVNTGRGTLIDEAALAEALKVGTIAAAGLDVYEREP-AVEA 271

Query: 269 PLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307
            L+ L N V LPH GSAT ETR AM    A+NL A   G
Sbjct: 272 ALIDLPNAVLLPHFGSATLETREAMGMKVADNLDAFFAG 310


Lambda     K      H
   0.317    0.131    0.366 

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: 219
Number of extensions: 12
Number of successful extensions: 3
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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