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 GFF377 Psest_0378 Lactate dehydrogenase and related dehydrogenases

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



>FitnessBrowser__psRCH2:GFF377
          Length = 309

 Score =  162 bits (410), Expect = 1e-44
 Identities = 105/255 (41%), Positives = 138/255 (54%), Gaps = 7/255 (2%)

Query: 47  GSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSL 106
           GS    +  ++     LKA+ +  VG+D  DV     RGI ++NTP+VL +  AD    L
Sbjct: 49  GSRFGCSAELMARLPALKAIVSFGVGYDPIDVPAAQARGIAISNTPEVLNDCVADLAMGL 108

Query: 107 ILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNM 166
           I+   R++     +V+AG W     P      V G  LGI+GLGRIG AVA+RA  GF+M
Sbjct: 109 IIDGRRQLSRADRFVRAGGWPSGNLP--LARRVTGSRLGILGLGRIGHAVAKRAE-GFSM 165

Query: 167 KVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSA 226
            V Y NR         Y    VELA     AD + L     P+T+ L+    L ++    
Sbjct: 166 PVRYHNRRPLADCPYEYAGSLVELARW---ADVLLLTCVGGPQTRGLVSREVLDALGPDG 222

Query: 227 ILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSAT 286
           +L+N +RG+ VDE AL+EALQ G + GA LDVF  EP   ++ LL + NVV LPHIGSAT
Sbjct: 223 LLVNVARGSVVDEPALVEALQAGRLGGAALDVFAEEPQAPEA-LLGMDNVVLLPHIGSAT 281

Query: 287 HETRHAMARNAAENL 301
            ETR AM      NL
Sbjct: 282 RETRGAMEDLVLANL 296


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: 215
Number of extensions: 17
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: 309
Length adjustment: 27
Effective length of query: 294
Effective length of database: 282
Effective search space:    82908
Effective search space used:    82908
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