GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas simiae WCS417

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF2935 PS417_15020 2-hydroxyacid dehydrogenase

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



>FitnessBrowser__WCS417:GFF2935
          Length = 317

 Score =  139 bits (351), Expect = 7e-38
 Identities = 87/246 (35%), Positives = 127/246 (51%), Gaps = 9/246 (3%)

Query: 62  RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWV 121
           +L+ +  I  G++  D+   + RGIV+ N   V   S AD   +L+L+  R + +    V
Sbjct: 67  QLEIICVIGAGYEHVDLQAASNRGIVVTNGAGVNAPSVADHAMALLLSLVRGIPQTDVAV 126

Query: 122 KAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEE 181
           + G W   + P+L      GK LGI+GLG +G  +A+RA+ GF M+V Y NR      + 
Sbjct: 127 RRGEWPKVMRPSL-----GGKQLGILGLGAVGLEIAKRASQGFGMEVSYHNRQPRDDVDY 181

Query: 182 AYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKA 241
            Y A  VELA    T+DF+ L  P    T+HLI    L ++  +  L+N  RG+ V    
Sbjct: 182 TYCATAVELAR---TSDFLILATPGGASTRHLIDRHALDALGPNGYLVNIGRGSVVVTAD 238

Query: 242 LIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENL 301
           L+ AL+   I GA LDVF+ EP   D+ L KL+N V   H+   + E  H   +  A+NL
Sbjct: 239 LVAALEQRRIGGAALDVFDDEPQVPDA-LKKLSNTVLTSHVAGLSPEAAHDTVQRVADNL 297

Query: 302 VAALDG 307
           V    G
Sbjct: 298 VEYFAG 303


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: 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: 317
Length adjustment: 28
Effective length of query: 293
Effective length of database: 289
Effective search space:    84677
Effective search space used:    84677
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