GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Streptacidiphilus oryzae TH49

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_037577639.1 BS73_RS30360 SDR family oxidoreductase

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



>NCBI__GCF_000744815.1:WP_037577639.1
          Length = 251

 Score =  143 bits (360), Expect = 4e-39
 Identities = 102/251 (40%), Positives = 134/251 (53%), Gaps = 14/251 (5%)

Query: 6   KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAF---GGTAIA 62
           +  IVTGASRGIGRA A   AR G  VV+ +      RA A + AE + A    G  A+A
Sbjct: 11  RLAIVTGASRGIGRAVAERLARDGTAVVVDY------RADAGAAAETVDAVHRAGARALA 64

Query: 63  VGADAADLDSGEKLVAAAVEAFGS-VDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGA 121
           V AD    D+   L  AA   FG   D+LV NAG+  F +  D+    Y     TN   A
Sbjct: 65  VPADVTSPDAPAVLFDAAERHFGRPADILVCNAGVARFGALADLSDADYDLVFDTNTRSA 124

Query: 122 YFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYG 181
           +   + A+RR+ +   GG I+ +SS +A+   A    Y  +KA   +LMQS A  LGP G
Sbjct: 125 FRLFREASRRLPD---GGRIVLMSSGAAVSRRAGSGIYAASKAAADALMQSLAKELGPRG 181

Query: 182 IRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVT 241
           I  N+VLPG + T+         E  ER+ +  PLGRLGEP D+A  + FL SD AR++T
Sbjct: 182 ITVNSVLPGAVRTEALAAR-GRPEVLERILADTPLGRLGEPGDIAEVVAFLTSDAARWLT 240

Query: 242 GASLLVDGGLF 252
           G +L   GG F
Sbjct: 241 GQTLHASGGEF 251


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: 169
Number of extensions: 12
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: 251
Length adjustment: 24
Effective length of query: 232
Effective length of database: 227
Effective search space:    52664
Effective search space used:    52664
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