GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Burkholderia vietnamiensis G4

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_011881868.1 3-hydroxybutyryl-CoA dehydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_000016205.1:WP_011881868.1
          Length = 261

 Score =  223 bits (567), Expect = 4e-63
 Identities = 115/258 (44%), Positives = 166/258 (64%), Gaps = 1/258 (0%)

Query: 3   FETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAF 61
           F+ I+ +K+  + ++T++RP  LNALN + L E+  A   A  D  +  +I+TG G KAF
Sbjct: 4   FQNIQYEKKSGIAYVTVDRPKSLNALNFQTLTEITAAFEDARDDDAVHGVIVTGSGNKAF 63

Query: 62  CAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121
            AGADI++   L+   A KF+  G   M+ IE L KP IA +NG+ALGGG ELA+AC +R
Sbjct: 64  VAGADISEIAALSAVAAEKFAGLGHSTMNLIETLGKPVIAAVNGFALGGGCELAMACTMR 123

Query: 122 IAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRV 181
           IA+E A+ G PE+ LGI PG+GGTQRL R++GKG A+++++T   I   +A + GLVN V
Sbjct: 124 IASEHAKFGQPEVKLGIIPGFGGTQRLPRLVGKGIAMQLILTAALIDANEAHRIGLVNEV 183

Query: 182 VPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDK 241
           V    L     ++  +IA  +PI+  L    VN+G+++ L   L+LE   + V  +TEDK
Sbjct: 184 VEADKLIARAEQILNQIAANAPIATRLAITAVNQGVEASLEQALSLERALFAVCAATEDK 243

Query: 242 KEGVSAFLEKREPTFKGK 259
            EG +AFL+KR PTF+ K
Sbjct: 244 AEGTAAFLDKRAPTFQSK 261


Lambda     K      H
   0.315    0.135    0.382 

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: 6
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: 259
Length of database: 261
Length adjustment: 24
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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 Apr 09 2024. 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