GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligK in Azospirillum brasilense Sp245

Align 4-carboxy-4-hydroxy-2-oxoadipic acid aldolase; CHA aldolase; Gallate degradation protein C; EC 4.1.3.17 (characterized)
to candidate AZOBR_RS25265 AZOBR_RS25265 4-hydroxy-4-methyl-2-oxoglutarate aldolase

Query= SwissProt::Q88JX9
         (238 letters)



>FitnessBrowser__azobra:AZOBR_RS25265
          Length = 224

 Score =  182 bits (461), Expect = 6e-51
 Identities = 94/213 (44%), Positives = 133/213 (62%)

Query: 14  NIPRVEPHMIDALGRLGVATVHEAQGRKGLLNTAVRPIQQGVAVAGSAVTVLVAPGDNWM 73
           + PR  P  + A   +G ATVHEA GR+G +++A++PI  G+ + G+A  +   PGDN  
Sbjct: 7   DFPRPTPEQVAAFATIGAATVHEALGRRGAVDSAIKPIWPGLRIVGAAFPLKTQPGDNLT 66

Query: 74  FHVAVEQCRPGDVLVVAPSSPCSDGYFGDLLATSLQARGVLGLVIDAGVRDSQTLRDMGF 133
            H A++  RPGDVLVV        G FGD++ATS Q+ G+ GLV + GVRD+  +RD+GF
Sbjct: 67  IHAAMKLARPGDVLVVDAGDYTEQGSFGDVMATSAQSLGLAGLVTNGGVRDAAAIRDIGF 126

Query: 134 AVWSRAINAQGTVKEVLGSVNLPLLCAGQLVNAGDIVVADDDGVVVVRHGEAQAVLEAAT 193
            ++SRAI+ +GTVK  LG +  P++  G  V+ GD++V DDDG+VVV   E +AVL A+ 
Sbjct: 127 PIFSRAISIKGTVKATLGPIAQPIVVGGVTVHPGDLIVGDDDGLVVVPLDEVEAVLTASR 186

Query: 194 QRADLEERKRLRLAAGELGLDIYEMRPRLAAKG 226
            R + EER R  L +G+   DI      LA  G
Sbjct: 187 ARLEKEERLRADLQSGKTTWDIGNYDALLAQTG 219


Lambda     K      H
   0.320    0.138    0.400 

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: 162
Number of extensions: 3
Number of successful extensions: 1
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: 238
Length of database: 224
Length adjustment: 23
Effective length of query: 215
Effective length of database: 201
Effective search space:    43215
Effective search space used:    43215
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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