GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araD in Azospirillum brasilense Sp245

Align L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) (characterized)
to candidate AZOBR_RS05280 AZOBR_RS05280 fuculose phosphate aldolase

Query= BRENDA::C4B4W3
         (240 letters)



>FitnessBrowser__azobra:AZOBR_RS05280
          Length = 232

 Score = 90.5 bits (223), Expect = 3e-23
 Identities = 64/199 (32%), Positives = 97/199 (48%), Gaps = 14/199 (7%)

Query: 42  TAGNVSQRVVVDKEAGPGPEDLFVIKPSGVSYDELTPEAMVVCNTEGDLIEGTRSPSSDT 101
           ++GN+S RV          E  F+I PS + YDE  PE +V    +G  + G R PSS+ 
Sbjct: 29  SSGNLSVRV----------EGGFLITPSSLPYDETAPEDIVEMGFDGTYV-GRRRPSSEW 77

Query: 102 AAHAYVYKHMDTVGGIVHTHSTYACAWAALGEEVPCVLTMMADEFGGPVPIGPFAIIGDD 161
             H  + K    V  ++HTHST+A A A  G  +P    M+A   G  +   P+A  G  
Sbjct: 78  RFHRDILKARPDVDVVLHTHSTFATALAVHGRGIPSFHYMVALAGGDSIRCAPYATFGSQ 137

Query: 162 SIGRGIVDTLKTSRSPAVLMKNHGPFTIGKDGRDAVKAAVMVEEVSKAAHLARTIGTPQI 221
            +    V  L+     A L+ NHG   +GK  + A+  AV VE +++    A  +G P I
Sbjct: 138 ELSDHAVAALEGRL--ACLLANHGMIVLGKTPKGALALAVEVETLARQYLHAHLLGEPVI 195

Query: 222 VPDEAIDALYDRYQNV-YG 239
           +P E I  + ++ + + YG
Sbjct: 196 LPPEEIARVAEKMRRMKYG 214


Lambda     K      H
   0.316    0.132    0.392 

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: 148
Number of extensions: 9
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: 240
Length of database: 232
Length adjustment: 23
Effective length of query: 217
Effective length of database: 209
Effective search space:    45353
Effective search space used:    45353
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 (21.6 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