GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Xanthobacter autotrophicus Py2

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_049776088.1 XAUT_RS04520 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>NCBI__GCF_000017645.1:WP_049776088.1
          Length = 258

 Score =  128 bits (321), Expect = 1e-34
 Identities = 82/247 (33%), Positives = 130/247 (52%), Gaps = 4/247 (1%)

Query: 12  ESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNR 71
           + E  + LTL+ P   NA   +++ +   ALD+   D + RAV++TGA   FCAG +L  
Sbjct: 6   QHEGWVELTLNRPDRLNAFTEELHRSLAAALDAAA-DDACRAVLLTGAGRGFCAGQDLGD 64

Query: 72  LLENRAKDPSVQAQSIDLLAE-WISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAAD 130
               +A+ P     +I+      I  +R   KPV+ AV+G AAGAG ++A ACD+++AA 
Sbjct: 65  --RAKAEGPLDLGATIEAFYNPLIRRIRALRKPVVCAVNGVAAGAGANIAFACDIVLAAR 122

Query: 131 DAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPG 190
            AKF+ ++A++GL PD GG++FL + +    A  +++  +P+ A +    G++ K     
Sbjct: 123 SAKFIQAFAKIGLVPDSGGTFFLPRLIGDARARALMLLAEPVSAEKAESWGLIWKAVDDA 182

Query: 191 TARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGI 250
              D A A A  L       +A  K  + A+    L   L  ERD    +    +  EG+
Sbjct: 183 ALMDEARALASHLASQPTQGLALTKQALNASAGNALDAQLDLERDLQREAGRTPDYREGV 242

Query: 251 SAFLEKR 257
           SAF+EKR
Sbjct: 243 SAFMEKR 249


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: 173
Number of extensions: 8
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: 258
Length adjustment: 24
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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 Apr 09 2024. 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