GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS13115 BWI76_RS13115
           2,3-dehydroadipyl-CoA hydratase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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