GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Pseudovibrio axinellae Ad2

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_068003992.1 PsAD2_RS06355 SDR family oxidoreductase

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



>NCBI__GCF_001623255.1:WP_068003992.1
          Length = 263

 Score =  162 bits (410), Expect = 7e-45
 Identities = 100/253 (39%), Positives = 140/253 (55%), Gaps = 9/253 (3%)

Query: 1   MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60
           M L  K  IVTG ++GIG A A+     GA+V+I  +    G A   +L+E    FG  A
Sbjct: 1   MKLDRKVAIVTGGAQGIGYAIAQRFLEDGAKVMISDADERAGEAAQEALSE----FGHVA 56

Query: 61  IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120
                    LD    +VA  ++ FG +DVLVNNAG+     FL +  + + + +  NL G
Sbjct: 57  FCHCDVGVRLDV-RNMVANTLDEFGDIDVLVNNAGVTAAGDFLTLSEDDFDRVLQVNLKG 115

Query: 121 AYFTVQAAARRMKEQ----GRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIA 176
           A+   QA AR M E+    G  G II +SS+++++    Q  YT +K GL  L    A+A
Sbjct: 116 AFLCSQAVARHMVEKIEEGGSAGIIINISSVNSVLAIPEQVPYTVSKGGLNQLTNVSAVA 175

Query: 177 LGPYGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDM 236
           L  YGIR N + PG+I TD+ K  + D  K  ++ SR PLGRLG+P ++AG   FLASD 
Sbjct: 176 LAKYGIRVNGIGPGSIETDMLKAVVQDESKMNKVLSRTPLGRLGQPSEIAGVASFLASDD 235

Query: 237 ARYVTGASLLVDG 249
           A YV+G ++  DG
Sbjct: 236 ASYVSGQTIFADG 248


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: 167
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: 263
Length adjustment: 24
Effective length of query: 232
Effective length of database: 239
Effective search space:    55448
Effective search space used:    55448
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