GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Skermanella stibiiresistens SB22

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_037454055.1 N825_RS16570 2-hydroxyacid dehydrogenase

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



>NCBI__GCF_000576635.1:WP_037454055.1
          Length = 325

 Score =  156 bits (395), Expect = 6e-43
 Identities = 98/279 (35%), Positives = 149/279 (53%), Gaps = 14/279 (5%)

Query: 30  TQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLA 89
           T+H A +  +       G    +  +++     L+ +    VG+DQ D       GIV+ 
Sbjct: 40  TEHGARIRGV-----AAGGHAGVDESLMARLPTLEIIGAFGVGYDQIDAKWAGEHGIVVT 94

Query: 90  NTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGL 149
           NTPDVLT+  AD    L+L++ R++      ++ G W     P      ++G+ +GI+GL
Sbjct: 95  NTPDVLTDEVADLTIGLLLSTVRQIPGAERHLREGKWPAGNYPLT--ASLRGRKVGILGL 152

Query: 150 GRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPE 209
           GRIG A+A+R    F + + Y  R      E  Y A  VELA  +   D +   +P    
Sbjct: 153 GRIGKAIAKRLQ-AFGLPISYYGRHKQDGVEFPYVADPVELARQV---DILISVLPGGAA 208

Query: 210 TKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEP-LPSDS 268
           T+ LIG+A  +++    + +N  RG+ VDE ALIEAL++ TI GAG+DVF  EP +P++ 
Sbjct: 209 TEKLIGSAVFEALGSDGVFVNVGRGSVVDEAALIEALRSKTILGAGIDVFADEPNVPAE- 267

Query: 269 PLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307
            L+   N V LPH+ SAT  TR+AM +   +NLV+  DG
Sbjct: 268 -LIARENAVLLPHVASATVHTRNAMGQLVVDNLVSWFDG 305


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: 248
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: 325
Length adjustment: 28
Effective length of query: 293
Effective length of database: 297
Effective search space:    87021
Effective search space used:    87021
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 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