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_RS17350 BPHYT_RS17350 enoyl-CoA hydratase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__BFirm:BPHYT_RS17350
          Length = 263

 Score =  132 bits (333), Expect = 6e-36
 Identities = 92/266 (34%), Positives = 135/266 (50%), Gaps = 9/266 (3%)

Query: 1   MSAELLTSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGAD 60
           MS E +      S     +TL+ P   N+    M+     ALD VE   + RA+V+TGA 
Sbjct: 1   MSYEAIRLDIDASSHVATITLNRPDKLNSFTRAMHQELSAALDQVETSGA-RALVLTGAG 59

Query: 61  NFFCAGGNLNRLLENRAKDPSVQAQSIDLLAEWISAL--RLSSKP--VIAAVDGAAAGAG 116
             FCAG +L  L       P       +L+ +  + L  RL + P  VIAAV+G AAGAG
Sbjct: 60  RGFCAGQDLADL----DFTPGAMTDLGELIEQHFNPLIRRLQALPLPVIAAVNGTAAGAG 115

Query: 117 FSLALACDLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAAR 176
            +LALACDL++AA  A F+ ++ ++GL PD GG+WFL Q +    A  + I G  + A +
Sbjct: 116 ANLALACDLVLAARSASFIQAFVKIGLVPDSGGTWFLPQRVGMARALGLAITGDKLSAEK 175

Query: 177 LHELGVVNKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDN 236
               G++ +        + A   A +L +    ++A IK  + A  TQ L + L  ERD 
Sbjct: 176 AESWGLIWQAVDDAELAETAAKLAAQLAQQPTRAIAAIKRAMRAGATQTLDQQLDLERDL 235

Query: 237 FVASLHHREGLEGISAFLEKRAPVYK 262
                   +  EG+ AF+EKRAP ++
Sbjct: 236 QRELGASHDYAEGVQAFVEKRAPRFE 261


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: 149
Number of extensions: 6
Number of successful extensions: 4
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: 263
Length adjustment: 25
Effective length of query: 237
Effective length of database: 238
Effective search space:    56406
Effective search space used:    56406
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