GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Flavobacterium glycines Gm-149

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_066330061.1 BLR17_RS12115 3-phosphoglycerate dehydrogenase

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



>NCBI__GCF_900100165.1:WP_066330061.1
          Length = 316

 Score =  124 bits (312), Expect = 2e-33
 Identities = 89/276 (32%), Positives = 142/276 (51%), Gaps = 24/276 (8%)

Query: 46  IGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFS 105
           + S+ K+   +++    LK +    VG D  DV     +GI + NTP   +ES A+ VF+
Sbjct: 48  VRSATKVRKDIIDACPGLKIIGRGGVGMDNIDVDYAKSKGIHVINTPASSSESVAELVFA 107

Query: 106 LILASAR------RVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARR 159
            +L   R      R + L    K    + +      GV+++GKTLGIVG+GRIG A A+ 
Sbjct: 108 HLLTGVRFLHDSNRNMPLEGDTKFNDLKKAYAN---GVELRGKTLGIVGIGRIGQATAKM 164

Query: 160 AALGFNMKVLYTNRSANPQAE---EAYGARRV-------ELAELLATADFVCLQVPLTPE 209
           A LG  MKV+  + S  PQ +   E +  + +        L  + A +DF+ L VP   +
Sbjct: 165 A-LGLGMKVIAAD-SFIPQVDVKVEFFDGQSITTTIKTQSLESVFAESDFITLHVPA--Q 220

Query: 210 TKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSP 269
             +++   E  +MK    ++N +RG  ++E  L++AL +G +  AGLDVFE EP P+ + 
Sbjct: 221 NGYIVTEKEFATMKNGVGIVNCARGGVINEVDLVKALDSGKVAFAGLDVFENEPTPA-TQ 279

Query: 270 LLKLANVVALPHIGSATHETRHAMARNAAENLVAAL 305
           LL    +   PHIG+AT E +  +    A  +++ L
Sbjct: 280 LLMHPKISLTPHIGAATGEAQDRIGTELASQIISIL 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: 203
Number of extensions: 10
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: 316
Length adjustment: 27
Effective length of query: 294
Effective length of database: 289
Effective search space:    84966
Effective search space used:    84966
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