GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Pseudomonas stutzeri RCH2

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF427 Psest_0431 Lactate dehydrogenase and related dehydrogenases

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



>FitnessBrowser__psRCH2:GFF427
          Length = 336

 Score =  160 bits (404), Expect = 5e-44
 Identities = 107/328 (32%), Positives = 167/328 (50%), Gaps = 14/328 (4%)

Query: 1   MKKIVAWKSLPEDVLAYLQQHAQVV--QVDAT-QHDAFVAALKDADGGIGSSV-KITPAM 56
           + K+V    + +++L  L  H +++  Q D+T   +  +   +DA   +     ++    
Sbjct: 2   LPKLVITHRVHDEILQLLAPHCELMTNQTDSTLPREEILRRCRDAQAMMAFMPDRVDADF 61

Query: 57  LEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVE 116
           L+    L+ +     GFD FDV   T RG+ L   PD+LT  TA+    L +   R +  
Sbjct: 62  LQACPELRVVGCALKGFDNFDVDACTARGVWLTFVPDLLTVPTAELAIGLAVGLGRHLRA 121

Query: 117 LAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSA- 175
              +V++G +Q    P  +G  +   T+GI+G+G IG A+A R   G+   + Y    A 
Sbjct: 122 ADAFVRSGKFQ-GWQPQFYGTGLDNATVGILGMGAIGLAMADRLQ-GWGATLQYHEAKAL 179

Query: 176 NPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGA 235
           + Q E+  G RRV  +EL A++DF+ L +PL  +T+HL+ A  L  ++  A+L+N  RG+
Sbjct: 180 DTQTEQRLGLRRVACSELFASSDFILLALPLNADTQHLVNAELLALVRPGALLVNPCRGS 239

Query: 236 TVDEKALIEALQNGTIHGAGLDVFETE-------PLPSDSPLLKLANVVALPHIGSATHE 288
            VDE A++ AL+ G + G   DVFE E       P   D  LL   N +  PHIGSA   
Sbjct: 240 VVDEAAVLAALERGQLGGYAADVFEMEDWARADRPRLIDPALLAHPNTLFTPHIGSAVRA 299

Query: 289 TRHAMARNAAENLVAALDGTLTSNIVNR 316
            R  + R AA+N++ AL G    N  NR
Sbjct: 300 VRLEIERCAAQNIIQALAGARPINAANR 327


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: 226
Number of extensions: 8
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: 336
Length adjustment: 28
Effective length of query: 293
Effective length of database: 308
Effective search space:    90244
Effective search space used:    90244
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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