GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Sporolactobacillus vineae SL153

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_026039138.1 RH97_RS13020 SDR family oxidoreductase

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



>NCBI__GCF_000246965.1:WP_026039138.1
          Length = 299

 Score =  122 bits (305), Expect = 1e-32
 Identities = 83/252 (32%), Positives = 128/252 (50%), Gaps = 8/252 (3%)

Query: 3   LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62
           L  K  +++G   GIGRAAA   AR+GARV I +   D+    A    + I A G   + 
Sbjct: 53  LTGKVAVISGGDSGIGRAAALAFAREGARVAIIYLNEDKD---AEWTKQRIEALGSECLP 109

Query: 63  VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGI-CPFHSFLDMPRELYLKTVGTNLNGA 121
           + AD  + ++ E + A  +  FG V +LVNN  +     S  ++  +  L T  TN+   
Sbjct: 110 IRADLRESEASETVAAQVIRHFGGVSILVNNCAVQFVRQSLTEISDDQLLNTFKTNIFSY 169

Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181
           ++  +A    +     G +II  +S++A  G      Y+ TK  ++SL +S +  L P G
Sbjct: 170 FYLTRAILPHLTS---GSSIINTASVTAYRGSKTLIDYSATKGAIVSLTRSLSQNLVPQG 226

Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241
           IR NAV PG I T +      + +K     + +P+ R G+P +LA   V+LASD +RY+T
Sbjct: 227 IRVNAVAPGPIWTPLIVASFKE-DKVGTFGTDMPMKRPGQPFELAPAYVYLASDDSRYMT 285

Query: 242 GASLLVDGGLFV 253
           G  L + GG  V
Sbjct: 286 GQVLHIGGGEMV 297


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: 159
Number of extensions: 10
Number of successful extensions: 4
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: 299
Length adjustment: 25
Effective length of query: 231
Effective length of database: 274
Effective search space:    63294
Effective search space used:    63294
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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