GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Paraburkholderia bryophila 376MFSha3.1

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate H281DRAFT_06500 H281DRAFT_06500 Lactate dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_06500
          Length = 308

 Score =  174 bits (441), Expect = 2e-48
 Identities = 105/261 (40%), Positives = 146/261 (55%), Gaps = 8/261 (3%)

Query: 48  SSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLI 107
           SS ++  ++L     LK ++T  VGFD   +     RG+++ NTP VL  +  +    L+
Sbjct: 49  SSYQVPASLLASLPNLKIIATSGVGFDGIPLDAARSRGVIVTNTPGVLDAAVCELAIGLL 108

Query: 108 LASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMK 167
           L+  RR+     +V+   W H + P    +   GK +GIVGLGRIG  +ARR A GF+++
Sbjct: 109 LSLLRRIPSADRFVRDEAWAHELFPLTSSL--AGKRIGIVGLGRIGQGIARRLA-GFDVE 165

Query: 168 VLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAI 227
           + Y       + E    A   ++ EL + AD + +  P    T+HLI  A L ++  S  
Sbjct: 166 IAY----CGSKVEGLPYAMISDVRELASFADILIVCCPGGDRTRHLIDGAVLSALGSSGF 221

Query: 228 LINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATH 287
           L+N SRG  VDE ALI+AL+ G I GA LDVFE EPL   S L  L+NVV  PH GSAT 
Sbjct: 222 LVNVSRGTVVDEAALIDALEKGLIRGAALDVFEKEPL-IGSRLATLSNVVLTPHAGSATE 280

Query: 288 ETRHAMARNAAENLVAALDGT 308
           ETRH M R A +N+   LDG+
Sbjct: 281 ETRHTMLRLALDNIHRVLDGS 301


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: 224
Number of extensions: 12
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: 308
Length adjustment: 27
Effective length of query: 294
Effective length of database: 281
Effective search space:    82614
Effective search space used:    82614
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