GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuE in Burkholderia phytofirmans PsJN

Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate BPHYT_RS03930 BPHYT_RS03930 3-hydroxy-3-methylglutaryl-CoA lyase

Query= SwissProt::O34873
         (299 letters)



>FitnessBrowser__BFirm:BPHYT_RS03930
          Length = 325

 Score =  190 bits (482), Expect = 4e-53
 Identities = 107/291 (36%), Positives = 165/291 (56%), Gaps = 7/291 (2%)

Query: 5   KKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAID 64
           ++V + EVG RDGLQ+    + TE K  WI+     G+ ++E+ SFV  K +P + DA +
Sbjct: 6   ERVVVTEVGMRDGLQSIARTMPTEFKRRWIDAAYAAGVRHMEVASFVPAKLLPQMADADE 65

Query: 65  VAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHI- 123
           V         +   ALVPN +G + ALE G++     +S S  H+  N+ ++ +E +   
Sbjct: 66  VIAHALTYDDLMVTALVPNLKGAQRALEAGVHRIVAPISVSSAHSLANVRRTPAEMIEAF 125

Query: 124 --LKQVNNDAQKAN---LTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGD 178
             +++  +   KA    +   A LSTVFGC  +  VP   +  ++ A  + G   ++LGD
Sbjct: 126 AAMRESIDGTSKAGGRRVELIAGLSTVFGCTLQGAVPYADIAAIARAAVQAGADVIALGD 185

Query: 179 TIGAANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLG 238
           T G A P QV  ++E +         +LHFHDTRG  LAN + ALQ GI  FD S  GLG
Sbjct: 186 TTGEATPRQVGEIIELVRDVVGGKLHSLHFHDTRGLGLANTLVALQHGIREFDASLAGLG 245

Query: 239 GCPYAPGSSGNAATEDIVYMLEQMDIKTNVKLEKLLSAAKWIEEKM-GKPL 288
           GCP+APG++GN  TED+V+ML+ M  +T + L++LL++   + + + G+PL
Sbjct: 246 GCPHAPGATGNVNTEDLVFMLDSMGYETGIDLDRLLASRAVLADALPGEPL 296


Lambda     K      H
   0.315    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: 206
Number of extensions: 8
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: 299
Length of database: 325
Length adjustment: 27
Effective length of query: 272
Effective length of database: 298
Effective search space:    81056
Effective search space used:    81056
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 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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