GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Herbaspirillum seropedicae SmR1

Align SDR family oxidoreductase (characterized, see rationale)
to candidate HSERO_RS19050 HSERO_RS19050 3-oxoacyl-ACP reductase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__HerbieS:HSERO_RS19050
          Length = 266

 Score =  127 bits (319), Expect = 2e-34
 Identities = 88/260 (33%), Positives = 141/260 (54%), Gaps = 17/260 (6%)

Query: 8   LAGKTVLITAAAQ-----GIGRASTELFAREGARVIATDIS-KTHLEE---LASIAGV-E 57
           + GK +++T A       G G+A+  L+AREG RV+A D S +  L+    + S  GV E
Sbjct: 5   MQGKAIIVTGAGSVGEGWGNGKAAAVLYAREGGRVLAVDRSIEAALQTQDIIRSEGGVCE 64

Query: 58  THLLDVTDDDAIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAM 113
               DV+ +  +KA+        G VDVL N  G    G  +E  +++W+    +N  ++
Sbjct: 65  VLAADVSRNTEVKAIAEAAMDHFGRVDVLHNNVGIADVGGPVETSEESWNRLVAVNQTSL 124

Query: 114 FHTIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQG 173
           F T + VLP M  ++ G+IVNI+S A+          Y A+KAA++  TK+VA  +   G
Sbjct: 125 FLTHKHVLPIMEKQRKGAIVNISSLAALRWIGFPYLGYTATKAAILAFTKNVAMQYAPMG 184

Query: 174 IRCNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYL 233
           IR N + PG +++P + + +       G   +++RA   A+ PMG +G A +VA  +L+L
Sbjct: 185 IRANCVLPGMMDTPMIREPLKA---SYGGDIEQMRAKRNAQCPMGFMGDAWDVAHASLFL 241

Query: 234 ASDESNFTTGSIHMIDGGWS 253
           ASD + + TG   ++DGG S
Sbjct: 242 ASDHARYITGLDMIVDGGLS 261


Lambda     K      H
   0.316    0.129    0.359 

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: 151
Number of extensions: 9
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: 254
Length of database: 266
Length adjustment: 24
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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