GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Burkholderia phytofirmans PsJN

Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate BPHYT_RS28880 BPHYT_RS28880 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase

Query= metacyc::MONOMER-16233
         (285 letters)



>FitnessBrowser__BFirm:BPHYT_RS28880
          Length = 252

 Score =  130 bits (326), Expect = 4e-35
 Identities = 76/215 (35%), Positives = 116/215 (53%), Gaps = 9/215 (4%)

Query: 53  EGEPRYGVPVKGIGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKN 112
           E E  +  P++ +G I A+GLNY +HA E       EP++F+K   ++ G       P +
Sbjct: 32  EDEVVWLAPIE-VGTIFALGLNYAEHAKELQFNKQEEPLVFLKGPGTVIGHRGVTRRPAD 90

Query: 113 STHGDWEVELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERFNQKQRGTQWSKGKGHDT 172
            T   +E EL VVIG+T + V  D A+  VAGY++ ND + R   +       + K  D 
Sbjct: 91  VTFMHYECELAVVIGQTAKNVKRDNAMQHVAGYMIANDYAIRDYLENYYRPNLRVKNRDG 150

Query: 173 FCPVGPWLVTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGD 232
              +GPW V   +V D   L++   VNGTR Q GNT+ ++  +  LI Y+S ++TL PGD
Sbjct: 151 GTVLGPWFVDAADVEDVTQLELRTFVNGTRQQHGNTRDLVTGIPALIEYLSSFMTLAPGD 210

Query: 233 LMITGTPPGVGEGKKPQAIYLKAGDVMELGIEKLG 267
           +++TGTP G+        + + AGD +   I+ LG
Sbjct: 211 VILTGTPEGI--------VNVNAGDEVVCEIDGLG 237


Lambda     K      H
   0.316    0.137    0.411 

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: 214
Number of extensions: 10
Number of successful extensions: 2
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: 285
Length of database: 252
Length adjustment: 25
Effective length of query: 260
Effective length of database: 227
Effective search space:    59020
Effective search space used:    59020
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: 42 (22.0 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