GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Nocardiopsis baichengensis YIM 90130

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_017559746.1 C892_RS0126925 phosphoglycerate dehydrogenase

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



>NCBI__GCF_000341205.1:WP_017559746.1
          Length = 529

 Score =  171 bits (432), Expect = 5e-47
 Identities = 106/302 (35%), Positives = 156/302 (51%), Gaps = 6/302 (1%)

Query: 15  LAYLQQHAQVVQVDATQHDAFVAALKDADGGI-GSSVKITPAMLEGATRLKALSTISVGF 73
           LA L+   +V           + AL D D  I  S+ ++    L  A +LK ++   VG 
Sbjct: 17  LALLEGDFEVRHTTGADRSQLLPALADVDALIVRSATQVDAEALAAAPKLKVVARAGVGL 76

Query: 74  DQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPA 133
           D  DV   T+ G+++ N P     S A+   +L+LASAR        +  G W+ S    
Sbjct: 77  DNVDVDAATKAGVLVVNAPTSNIISAAEQAVNLLLASARNTAPAHNALVNGEWKRS---K 133

Query: 134 LFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAEL 193
             GV+V  KT+G+VGLGRIG  VA+R A  F  K++  +    P      G   V L EL
Sbjct: 134 YTGVEVYDKTVGVVGLGRIGALVAQRLA-AFGTKLIAYDPFVQPARAAQMGVEMVSLDEL 192

Query: 194 LATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHG 253
           L  +DF+ + +P + +T  LIG   L  +K S  +INA+RG  +DE AL  A++ G + G
Sbjct: 193 LQRSDFITVHLPKSKDTLGLIGDEALHKVKPSVRVINAARGGILDEDALYRAIKEGRVAG 252

Query: 254 AGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNI 313
           AG+DV+ +EP  +DSPL +  NVV  PH+G++THE +         ++  AL G    + 
Sbjct: 253 AGIDVWASEPC-TDSPLFEFENVVVAPHLGASTHEAQEKAGTQVVRSVKLALAGEFVPDA 311

Query: 314 VN 315
           VN
Sbjct: 312 VN 313


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: 343
Number of extensions: 13
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: 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 Sep 24 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