GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Acidovorax sp. GW101-3H11

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate Ac3H11_1055 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1055
          Length = 259

 Score =  292 bits (747), Expect = 5e-84
 Identities = 156/262 (59%), Positives = 190/262 (72%), Gaps = 3/262 (1%)

Query: 1   MSAELLTSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGAD 60
           M AEL   R T    TL+LTLSNP  RNA+ P MYAAG+EAL   E    IR+VVITG+D
Sbjct: 1   MPAEL---RSTSQGQTLILTLSNPERRNAIDPSMYAAGVEALSVAESSADIRSVVITGSD 57

Query: 61  NFFCAGGNLNRLLENRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLA 120
             FC+GGNL RLL NR   P VQAQSI+ L  WI  +R   KPVIAAV+GAAAGAGFSLA
Sbjct: 58  GMFCSGGNLQRLLANRQLPPDVQAQSIEGLHNWIETIRTYPKPVIAAVEGAAAGAGFSLA 117

Query: 121 LACDLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHEL 180
           LACD IVAA +A FVM+Y+ V L+PDGG SW L+QALPRQ+ATE+L+ G  IGA RLH L
Sbjct: 118 LACDFIVAARNAVFVMAYSNVALSPDGGASWSLSQALPRQIATEILMCGDRIGAERLHAL 177

Query: 181 GVVNKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVAS 240
           G+VN++ + G+A DAA+A A++L   +PN++A IK L+  A    L++HL  ERD+FV +
Sbjct: 178 GLVNRVAEAGSALDAALALAEQLNAKAPNALASIKELLNEAPHASLTQHLGHERDHFVKN 237

Query: 241 LHHREGLEGISAFLEKRAPVYK 262
           LHH  G  GISAFLEKR P Y+
Sbjct: 238 LHHANGGAGISAFLEKRVPRYE 259


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: 205
Number of extensions: 4
Number of successful extensions: 1
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: 259
Length adjustment: 25
Effective length of query: 237
Effective length of database: 234
Effective search space:    55458
Effective search space used:    55458
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