GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Burkholderia phytofirmans PsJN

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate BPHYT_RS28620 BPHYT_RS28620 enoyl-CoA hydratase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__BFirm:BPHYT_RS28620
          Length = 260

 Score =  139 bits (349), Expect = 8e-38
 Identities = 86/245 (35%), Positives = 138/245 (56%), Gaps = 10/245 (4%)

Query: 19  LTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENRAK 78
           +TL+ P  RNA+  DM    IEAL+ V  DP +RAVV+TG+   FCAGG++  + + R +
Sbjct: 17  ITLNRPEKRNAISDDMRTELIEALNRVSTDPEVRAVVLTGSGKGFCAGGDVGGMAK-RME 75

Query: 79  DPSVQA-----QSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAK 133
            P+ +           +   ++ L    KP IAAV+GAAAG G  +AL+CD +VA+++A 
Sbjct: 76  APAGEVAFNGWSRQQRVHHTVNLLFSMPKPTIAAVNGAAAGLGADMALSCDFVVASEEAS 135

Query: 134 FVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTAR 193
           F  SY + GL PDGGG +FL + +    A E++  G+ + A     LG+ +++++     
Sbjct: 136 FAWSYIKRGLIPDGGGMYFLPRRVGLSRAKELIFSGRKVEAPEALALGIADRVSRSDALL 195

Query: 194 DAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHH--REGLEGIS 251
             A AWA+EL + SP ++A  K+++    +  LS H V  + +   ++ +   E  E + 
Sbjct: 196 ADAQAWAEELAQGSPTALALGKSIL--NQSYELSAHQVFAQGSQAQAVCYTSHEHRESVL 253

Query: 252 AFLEK 256
           AFL K
Sbjct: 254 AFLNK 258


Lambda     K      H
   0.317    0.132    0.377 

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: 150
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: 262
Length of database: 260
Length adjustment: 25
Effective length of query: 237
Effective length of database: 235
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: 41 (21.7 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