GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Herbaspirillum seropedicae SmR1

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate HSERO_RS02535 HSERO_RS02535 short-chain dehydrogenase

Query= metacyc::MONOMER-16230
         (256 letters)



>FitnessBrowser__HerbieS:HSERO_RS02535
          Length = 249

 Score =  169 bits (429), Expect = 4e-47
 Identities = 105/258 (40%), Positives = 151/258 (58%), Gaps = 13/258 (5%)

Query: 1   MLLIDKTVIVTGAS--RGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGG 58
           MLL DK  I+TG +   G+G + AR  A QGAR+VI     D  RA     A   A  G 
Sbjct: 1   MLLKDKVAIITGGAGQNGLGFSTARLMAAQGARIVI----LDLERAEPAGAA---ARLGA 53

Query: 59  TAIAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNL 118
             + + AD  D  + E   AA ++ FG +D+LVNNAG+      L++  + Y + +  +L
Sbjct: 54  QHLGLVADVTDKAACEAAAAAVLKQFGRIDILVNNAGVTQPAKLLEITGKDYDRILDVSL 113

Query: 119 NGAYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQ--THYTPTKAGLLSLMQSCAIA 176
            G  +  QA    M+ Q + G+I+ +SS+SA  GG +    HY+  KAG+L L ++ A  
Sbjct: 114 RGTLYMSQAVLPAMQAQ-QSGSIVCISSVSAQRGGGILGGPHYSAAKAGVLGLARAMARE 172

Query: 177 LGPYGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDM 236
            GP GIR N + PG I+TDINK+ LS  EK+  +   +PLGRLG PDD+ G  VFLASD+
Sbjct: 173 FGPQGIRVNCITPGLISTDINKDILS-AEKKAEIAQTIPLGRLGGPDDVGGVCVFLASDL 231

Query: 237 ARYVTGASLLVDGGLFVN 254
           ++Y TG +L V+GG+ ++
Sbjct: 232 SQYCTGVTLDVNGGMLIH 249


Lambda     K      H
   0.319    0.136    0.383 

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: 197
Number of extensions: 14
Number of successful extensions: 5
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: 256
Length of database: 249
Length adjustment: 24
Effective length of query: 232
Effective length of database: 225
Effective search space:    52200
Effective search space used:    52200
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.

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