GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Burkholderia phytofirmans PsJN

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BPHYT_RS20960 BPHYT_RS20960 dihydrofolate reductase

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



>FitnessBrowser__BFirm:BPHYT_RS20960
          Length = 320

 Score =  159 bits (403), Expect = 7e-44
 Identities = 105/245 (42%), Positives = 134/245 (54%), Gaps = 6/245 (2%)

Query: 63  LKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVK 122
           +K ++  S GFD  DVA    RGIV+ N PD LTE TAD    L+LA+ RR  E    ++
Sbjct: 73  VKIIANASAGFDHMDVAAARERGIVVTNAPDALTECTADFSLLLVLAACRRASEYERIMR 132

Query: 123 AGHWQHSIGPA-LFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEE 181
            G W  S G   + G  V GKTLGIVG GRIG AVA+RA  GF M+V+YT+ +    + E
Sbjct: 133 NG-WGKSFGMTEMLGTRVNGKTLGIVGFGRIGRAVAKRAQ-GFGMRVIYTDINRAAASLE 190

Query: 182 AYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKA 241
                   L E+L     + L VP       L+   E   +   A+ +NA+RGA VDE A
Sbjct: 191 NGATFYNSLDEMLPHCQVLTLHVP--GGGVPLMTKREFALLPAGAVFVNAARGALVDEDA 248

Query: 242 LIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENL 301
           L EAL +G + GAGLDV+  EP   D     L NV   PH+ SAT ETR  M   A +N+
Sbjct: 249 LYEALTSGHLFGAGLDVYRNEP-NVDKRFAGLDNVFLTPHMASATMETRDQMGFTALDNV 307

Query: 302 VAALD 306
            A L+
Sbjct: 308 AAVLN 312


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: 229
Number of extensions: 13
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: 320
Length adjustment: 28
Effective length of query: 293
Effective length of database: 292
Effective search space:    85556
Effective search space used:    85556
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