GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Collinsella tanakaei YIT 12063

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_009141108.1 HMPREF9452_RS05340 phosphoglycerate dehydrogenase

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



>NCBI__GCF_000225705.1:WP_009141108.1
          Length = 326

 Score =  173 bits (439), Expect = 4e-48
 Identities = 110/275 (40%), Positives = 153/275 (55%), Gaps = 8/275 (2%)

Query: 40  KDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTEST 99
           KDAD  I  + ++  A +   + LK +     G D  D ++L +R I +ANTP    E T
Sbjct: 51  KDADVIILGNDRLDSATIGKLSNLKLVVRHGAGLDNIDFSELGKRDITVANTPGANKEET 110

Query: 100 ADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARR 159
           AD  F+LIL  AR V +    +K G W    G  L+G     KT+GI+G+G IG AVA R
Sbjct: 111 ADLTFALILDLARMVTQSINQLKGGVWNKIPGRTLYG-----KTIGIIGVGAIGMAVASR 165

Query: 160 AALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAEL 219
           A +GF M +L  +     +A   +G     L ELL+ +D V + VPLT  TK+LIGA EL
Sbjct: 166 A-MGFGMDILGNDIVQRDEAAR-FGLLYTSLNELLSASDVVTIHVPLTSATKNLIGAREL 223

Query: 220 KSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVAL 279
           K MK  A+LIN +R   V E AL +AL +G + G  +DV+  EP P  +  + L NV+  
Sbjct: 224 KRMKPDALLINTARAGVVREAALEKALMSGHLGGYAVDVYVKEP-PDPTSYMSLPNVLTT 282

Query: 280 PHIGSATHETRHAMARNAAENLVAALDGTLTSNIV 314
           PHIGS+T E    M   A +N++A ++G +  N V
Sbjct: 283 PHIGSSTMEANLRMGDMAVDNILAFMNGAVLPNKV 317


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: 217
Number of extensions: 5
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: 326
Length adjustment: 28
Effective length of query: 293
Effective length of database: 298
Effective search space:    87314
Effective search space used:    87314
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