GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Azospirillum brasilense Sp245

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate AZOBR_RS15695 AZOBR_RS15695 dihydrofolate reductase

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



>FitnessBrowser__azobra:AZOBR_RS15695
          Length = 312

 Score =  157 bits (397), Expect = 3e-43
 Identities = 97/261 (37%), Positives = 141/261 (54%), Gaps = 7/261 (2%)

Query: 47  GSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSL 106
           G    ++ A+++    L  ++   VG D  D+     RG+ + NTPDVLT+  AD    L
Sbjct: 51  GGGTGVSNAIMDACPNLGIVAINGVGTDAVDLKHAAGRGVRVTNTPDVLTDDVADLAIGL 110

Query: 107 ILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNM 166
           ++A +RR++    +V+AG W    G       V GK LGI+GLGRIG A+A+RAA GF M
Sbjct: 111 MIAGSRRMMVGDRFVRAGRWPG--GGLPLARKVTGKRLGILGLGRIGMAIAQRAA-GFGM 167

Query: 167 KVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSA 226
            + YTNR         + A  V+LA     +D + +     P+ ++++  A ++++    
Sbjct: 168 DIAYTNRKPRSDVPYRFVASPVDLAR---ESDILIVAASAGPDARNMVNRAVIEALGPDG 224

Query: 227 ILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSAT 286
           +L+N +RGA VDE  L+ AL +G + GA LDVF  EP   ++ L  L NVV  PH  SAT
Sbjct: 225 LLVNVARGAVVDEPELVAALADGRLGGAALDVFANEPHAPEA-LFGLDNVVLQPHQASAT 283

Query: 287 HETRHAMARNAAENLVAALDG 307
            ETR AM      NL A   G
Sbjct: 284 VETRMAMGNLVLANLSAFFAG 304


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: 240
Number of extensions: 14
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 321
Length of database: 312
Length adjustment: 27
Effective length of query: 294
Effective length of database: 285
Effective search space:    83790
Effective search space used:    83790
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