GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Burkholderia phytofirmans PsJN

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate BPHYT_RS28020 BPHYT_RS28020 enoyl-CoA hydratase

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__BFirm:BPHYT_RS28020
          Length = 272

 Score =  160 bits (404), Expect = 3e-44
 Identities = 94/244 (38%), Positives = 137/244 (56%), Gaps = 2/244 (0%)

Query: 11  EGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADISE 70
           +G VA +T+ RP A NA   + L ++   +  +  ++ V A+++TG G K F AGAD++ 
Sbjct: 9   DGAVAQLTLKRPPA-NAFTPEGLLQLQQTVERLNGEARVRAIVITGDGPKFFSAGADLNT 67

Query: 71  MKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIASSNARF 130
             + N    R         F  L+     VIAA+NG+A+GGG E A++CDIRIA  +A  
Sbjct: 68  FADGNREVARTAAARFGAAFETLQNARPVVIAAINGYAMGGGLECALACDIRIAEQHALL 127

Query: 131 GQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEPSELMN 190
             PE  +G+ P   GTQ L  LVG G AK++I T + + A  ALRIGLV +VVE     +
Sbjct: 128 ALPETAVGLLPCGCGTQTLPWLVGEGWAKRMILTGERVDAATALRIGLVEEVVEKGAARD 187

Query: 191 TAKEIANKIVSNAPVAVKLSKQAINRGMQ-CDIDTALAFESEAFGECFSTEDQKDAMTAF 249
            A  +A ++ + +P AV  SK  I++G        ALA E E F + F   DQ++ + AF
Sbjct: 188 AALVMAARVATLSPQAVGFSKTLIHQGRSGVPRAAALALERERFVDLFDGADQREGVNAF 247

Query: 250 IEKR 253
           +EKR
Sbjct: 248 LEKR 251


Lambda     K      H
   0.317    0.134    0.365 

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: 161
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: 261
Length of database: 272
Length adjustment: 25
Effective length of query: 236
Effective length of database: 247
Effective search space:    58292
Effective search space used:    58292
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: 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