GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Burkholderia phytofirmans PsJN

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate BPHYT_RS10815 BPHYT_RS10815 crotonase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__BFirm:BPHYT_RS10815
          Length = 268

 Score =  149 bits (375), Expect = 8e-41
 Identities = 88/246 (35%), Positives = 134/246 (54%), Gaps = 13/246 (5%)

Query: 17  ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTPA 76
           I L+RP  LN ++    ++L  A    + DP +RVI++  KG+ F +G DI  F + +P 
Sbjct: 31  IILHRPP-LNVISMHARDQLRAAFEALDDDPRVRVIVVRAKGEHFSSGGDIKGFLEASPE 89

Query: 77  E----AWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLP 132
                AW  +   R         SKP IA   G+  G G EL+LACD RIA +     LP
Sbjct: 90  TVSKLAWNIAAPAR--------CSKPVIAANRGFCFGVGFELSLACDFRIATDTTFYALP 141

Query: 133 EINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETR 192
           E  LG  PG GG+ RL +++G GR  +++M   RIPGK A ++G+    V  + LE  T 
Sbjct: 142 EQKLGQIPGSGGSARLQQMVGIGRTKDIVMRSRRIPGKQAYEWGIAVECVADSELEAATD 201

Query: 193 KLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKR 252
            L +++   SP++    K+++N   D+PL   + LE   +  + +++D +EGV AF  KR
Sbjct: 202 ALVDELRAFSPLAQRTAKKLLNDTEDAPLSIAIELEGHCYSRLRASDDFREGVEAFHGKR 261

Query: 253 EPTFKG 258
           +P F+G
Sbjct: 262 KPVFRG 267


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: 135
Number of extensions: 3
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: 268
Length adjustment: 25
Effective length of query: 234
Effective length of database: 243
Effective search space:    56862
Effective search space used:    56862
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