GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 in Klebsiella michiganensis M5al

Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase

Query= uniprot:A0A2Z5MCI7
         (262 letters)



>FitnessBrowser__Koxy:BWI76_RS13115
          Length = 255

 Score =  128 bits (321), Expect = 1e-34
 Identities = 82/246 (33%), Positives = 131/246 (53%), Gaps = 5/246 (2%)

Query: 17  LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENR 76
           L LTL+ P ARNAL+  +     + LD+   DP++   VI+G + FF AG +LN + EN 
Sbjct: 13  LQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAGADLNEMAEN- 71

Query: 77  AKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVM 136
                + A   D+     + +   SKP+IA+V+G A GAG  LAL CDLIVA D+A+F +
Sbjct: 72  ----DLPATLDDIRPRLWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDNARFGL 127

Query: 137 SYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAA 196
               +G+ P  GG+  L +++ + LA+ +++ G+ I A +    G+V+++  P    + A
Sbjct: 128 PEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPALTDEYA 187

Query: 197 VAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEK 256
           ++ A  + + SP ++   K  +  +    L   L  ER  F       +  EGI AFL K
Sbjct: 188 LSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATEDRREGIDAFLHK 247

Query: 257 RAPVYK 262
           R   +K
Sbjct: 248 RTAEFK 253


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: 133
Number of extensions: 9
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: 255
Length adjustment: 24
Effective length of query: 238
Effective length of database: 231
Effective search space:    54978
Effective search space used:    54978
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