GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Mucilaginibacter mallensis MP1X4

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_091375988.1 BLU33_RS17605 phosphoglycerate dehydrogenase

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



>NCBI__GCF_900105165.1:WP_091375988.1
          Length = 311

 Score =  136 bits (343), Expect = 6e-37
 Identities = 87/227 (38%), Positives = 114/227 (50%), Gaps = 6/227 (2%)

Query: 62  RLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWV 121
           +L+      VG D  D     + GI ++NTP +     AD   +     AR    +   V
Sbjct: 71  KLRVAVKWGVGVDNVDFKACEKLGIPISNTPRMFGNEVADMALAYFTGLARESYRVDREV 130

Query: 122 KAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEE 181
           +AG+W   I PA  G+ + GKT+ ++G+G IG A ARR    F +K+   +      A E
Sbjct: 131 RAGNW---IKPA--GMSLDGKTVALIGVGDIGLATARRLK-AFGVKINAYDPFTKLTAAE 184

Query: 182 AYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKA 241
           A     +   + L  ADFV L   LTP   HLI A  +  MK   I+IN SRG  +DE A
Sbjct: 185 ANVDEILAFPDKLEQADFVLLTCALTPSNFHLINAESIAKMKDGVIVINVSRGGLIDETA 244

Query: 242 LIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHE 288
           L  AL +G +  AGLDVFETEPLP DSPL      +   H GS T E
Sbjct: 245 LTAALTSGKVRSAGLDVFETEPLPMDSPLRSFEQCILGTHNGSNTRE 291


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: 202
Number of extensions: 5
Number of successful extensions: 2
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: 311
Length adjustment: 27
Effective length of query: 294
Effective length of database: 284
Effective search space:    83496
Effective search space used:    83496
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