GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Erythrobacter marinus HWDM-33

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_047093910.1 AAV99_RS08330 3-hydroxybutyrate dehydrogenase

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_001013305.1:WP_047093910.1
          Length = 251

 Score =  139 bits (350), Expect = 5e-38
 Identities = 95/253 (37%), Positives = 138/253 (54%), Gaps = 23/253 (9%)

Query: 10  GRCAIVTGGASGLGKQVAARIIAEGGAVALWDL-NGDALAATQAEIDATHVVA--LDVSD 66
           G+ A+VTG  SG+G  +A  + AEG +V +    + D +A   AEI ATH  A  +DV +
Sbjct: 5   GKRALVTGSTSGIGLAIAKALAAEGASVVINGFGDADEIAGICAEIGATHSGANLMDVGE 64

Query: 67  HAAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREV 126
              + A A       G +DIL+ +AG+     PV EFPV+ + +VI +NL  +F+  R  
Sbjct: 65  IETMMAEA-------GPLDILVNNAGMQHVC-PVEEFPVEKWHQVIALNLTAVFHTTRLA 116

Query: 127 VPFMLENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTP 186
           VP M E G+GRI+N AS   K  +P  SAY+ASK GV GFTK++  ELA  GV AN ++P
Sbjct: 117 VPAMREKGWGRIINTASAHSKTASPFKSAYNASKHGVDGFTKTVALELAETGVTANCISP 176

Query: 187 ATFESPILD-QLP---------QSQV--DYMRSKIPMGRLGLVEESAAMVCFMASEECSF 234
               +P+++ Q+P         + QV  D + +K P  +   VEE  A+  F+   E   
Sbjct: 177 GYVWTPLIEGQIPDTMKARGLTEEQVINDVLLAKQPTKKFVQVEEVGALATFLCRTEMGN 236

Query: 235 TTASTFDTSGGRT 247
            T + +   GG T
Sbjct: 237 VTGANWSIDGGWT 249


Lambda     K      H
   0.318    0.132    0.381 

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: 147
Number of extensions: 8
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: 249
Length of database: 251
Length adjustment: 24
Effective length of query: 225
Effective length of database: 227
Effective search space:    51075
Effective search space used:    51075
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: 46 (22.3 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