GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF377 Psest_0378 Lactate dehydrogenase
           and related dehydrogenases
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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