GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Methanococcus aeolicus Nankai-3

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_011973284.1 MAEO_RS02815 phosphoglycerate dehydrogenase

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



>NCBI__GCF_000017185.1:WP_011973284.1
          Length = 523

 Score =  202 bits (514), Expect = 1e-56
 Identities = 117/316 (37%), Positives = 176/316 (55%), Gaps = 6/316 (1%)

Query: 1   MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEG 59
           M KI+   S+ +D +  L+Q   V        +     +KDAD   I S  K T  +++ 
Sbjct: 1   MPKILITDSIHDDAVELLKQAGTVEVATDLTVEELKEKIKDADALVIRSGTKATKEIIDA 60

Query: 60  ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119
           A  LK ++   VG D  D+   T +GI++ N+PD  + S A+    L+L+SAR + +   
Sbjct: 61  ADNLKVIARAGVGVDNVDLTAATEKGIIVVNSPDASSISVAELALGLMLSSARNIPQATA 120

Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179
            +K G W      +  G+++ GKTLGI+GLGRIG  +A+RA   F M V+  +     + 
Sbjct: 121 SLKRGEWDRK---SFKGMELYGKTLGIIGLGRIGQQIAKRAE-AFGMTVVAYDPYIPVEV 176

Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239
            +  G   +E+ +L   +DF+ L VPLTP+TKH+IG  ++  MK + I++N +RG  +DE
Sbjct: 177 AKNMGIELMEVNDLCKVSDFITLHVPLTPKTKHMIGKEQISLMKPNTIIVNCARGGLIDE 236

Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAE 299
           +AL +A+ N  I GAGLDVFE EP P D+PLL L   +  PH G++T E + +     AE
Sbjct: 237 EALYDAINNKKIGGAGLDVFEEEP-PKDNPLLTLDKFIGTPHQGASTVEAQKSAGTVVAE 295

Query: 300 NLVAALDGTLTSNIVN 315
            +V  L G    NIVN
Sbjct: 296 QVVKILAGKPADNIVN 311


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: 328
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: 523
Length adjustment: 31
Effective length of query: 290
Effective length of database: 492
Effective search space:   142680
Effective search space used:   142680
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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