GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Azospirillum brasilense Sp245

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate AZOBR_RS09410 AZOBR_RS09410 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase

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



>FitnessBrowser__azobra:AZOBR_RS09410
          Length = 253

 Score =  171 bits (434), Expect = 1e-47
 Identities = 105/252 (41%), Positives = 143/252 (56%), Gaps = 5/252 (1%)

Query: 3   LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62
           L ++T +VTGAS G+GR  A   A  GARV +    +   R    +   EI A GG AIA
Sbjct: 5   LTNRTALVTGASAGLGRHFAGVLAAAGARVAL----AARRRESLDAAVAEIEAAGGQAIA 60

Query: 63  VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122
           V  D  D  S    V  A  A G +D+LVNNAG       LD   E + + + TNL GA+
Sbjct: 61  VPLDVTDAASVRNGVREAAGALGGLDILVNNAGATVAKPALDYAEEEWDRVIDTNLKGAF 120

Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182
            T Q  AR M+EQGRGG+I+ ++SI  L        YT +KAGL+ + Q+ A+    YGI
Sbjct: 121 LTAQETARVMREQGRGGSIVNIASILGLRVAGHVVAYTASKAGLVQMTQAVALEWARYGI 180

Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242
           R NA+ PG + TD+N++ L+  +  + +  RVP  RLG   DL GP++ L SD + Y+TG
Sbjct: 181 RVNALAPGYMETDLNRDFLA-TDAGQALIRRVPQRRLGRLADLDGPLLLLCSDASAYMTG 239

Query: 243 ASLLVDGGLFVN 254
           A + VDGG  V+
Sbjct: 240 AVVPVDGGHLVS 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: 182
Number of extensions: 7
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: 256
Length of database: 253
Length adjustment: 24
Effective length of query: 232
Effective length of database: 229
Effective search space:    53128
Effective search space used:    53128
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 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