GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Desulfoscipio geothermicus DSM 3669

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_092487414.1 BM299_RS17355 phosphoglycerate dehydrogenase

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



>NCBI__GCF_900115975.1:WP_092487414.1
          Length = 529

 Score =  192 bits (488), Expect = 2e-53
 Identities = 115/316 (36%), Positives = 177/316 (56%), Gaps = 8/316 (2%)

Query: 3   KIVAWKSLPEDVLAYLQQHAQVVQVDATQ--HDAFVAALKDADGGI-GSSVKITPAMLEG 59
           K++A  ++ E  L  L++   +  V   +   D  V  + D D  I  S+ K+TP +LE 
Sbjct: 5   KVLAMDNVSEKGLEPLRKEPDIEVVIGKKMTEDELVEIIGDYDAMIVRSATKVTPRVLEN 64

Query: 60  ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119
           A +LK +    VG D  D+   T+ G+++ N PD  T +  +   +++LA AR + +   
Sbjct: 65  APKLKVVGRAGVGVDNIDLNAATQHGVLVVNAPDGNTIAATEHTIAMMLALARNIPQAVA 124

Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179
            +K G W      A  GV+++GK LG++GLGRIG AVARRA     M ++  +     + 
Sbjct: 125 KMKNGVWDKK---AFLGVELRGKVLGVIGLGRIGSAVARRAQ-ALEMDIVAYDPYITSEK 180

Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239
            E+ G + V + ELL  ADF+ + +P T ET H++       MK    +IN +RG  VDE
Sbjct: 181 AESLGIKLVTMDELLPVADFITMHMPKTKETYHMLDEQAFAKMKDGVRVINCARGGIVDE 240

Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAE 299
           +AL + +Q+G + GA LDVFE EP  ++SPLL L N +A PH+G++T E +  +A + AE
Sbjct: 241 EALYKYMQSGKVAGAALDVFEKEP-NTESPLLALDNFIATPHLGASTAEAQLNVAIDVAE 299

Query: 300 NLVAALDGTLTSNIVN 315
            +V AL G +  N VN
Sbjct: 300 EIVEALQGKVVRNTVN 315


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: 342
Number of extensions: 18
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: 321
Length of database: 529
Length adjustment: 31
Effective length of query: 290
Effective length of database: 498
Effective search space:   144420
Effective search space used:   144420
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