GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Cupriavidus basilensis 4G11

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate RR42_RS23450 RR42_RS23450 enoyl-CoA hydratase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__Cup4G11:RR42_RS23450
          Length = 264

 Score =  131 bits (330), Expect = 1e-35
 Identities = 83/245 (33%), Positives = 125/245 (51%), Gaps = 4/245 (1%)

Query: 18  VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLN---RLLE 74
           V+ L+ P  RNA+  DM    I+AL+ V  D ++RA+VITG    FCAGG+++   R +E
Sbjct: 17  VIALNRPEKRNAMSDDMRTEFIDALERVAADKAVRALVITGNGKGFCAGGDVSGMKRRME 76

Query: 75  NRAKDPSVQAQSIDLLAEWISAL-RLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAK 133
               +      S      +   L     KP +AAV+GAAAG G   AL CD ++A++ A 
Sbjct: 77  APQGEVGFNGWSRQQRVHYTQKLLHTMPKPTVAAVNGAAAGLGADTALCCDFVIASEHAS 136

Query: 134 FVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTAR 193
           F  SY   GL PDGGG +FL + +    A E++  G+ +      E+G+V++++   +  
Sbjct: 137 FSWSYINRGLIPDGGGMYFLPRRVGLAKAKELVFTGRKVAIEEAKEIGIVDRVSHADSLV 196

Query: 194 DAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAF 253
             AVAWA EL + SP ++A  KT++  +   P  +                E  E + AF
Sbjct: 197 ADAVAWAKELSQGSPTAIALGKTIMNQSYELPADQIFAQGSQAQGICYTSAEHRESVLAF 256

Query: 254 LEKRA 258
           L K A
Sbjct: 257 LNKLA 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: 141
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: 264
Length adjustment: 25
Effective length of query: 237
Effective length of database: 239
Effective search space:    56643
Effective search space used:    56643
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