GapMind for catabolism of small carbon sources

 

Aligments for a candidate for badK in Klebsiella michiganensis M5al

Align BadK (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS13115 BWI76_RS13115
           2,3-dehydroadipyl-CoA hydratase
          Length = 255

 Score =  185 bits (470), Expect = 7e-52
 Identities = 112/246 (45%), Positives = 145/246 (58%), Gaps = 1/246 (0%)

Query: 13  RVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAA 72
           RV  +TLNRP   NALN+AL+  +   L A   D  +G  VI+GN R FAAGAD+  MA 
Sbjct: 11  RVLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAGADLNEMAE 70

Query: 73  WSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALPE 132
                    +   R W  I    KP++A+V G A G GCELAL CD+++AG +A+F LPE
Sbjct: 71  NDLPATL-DDIRPRLWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDNARFGLPE 129

Query: 133 IKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETVA 192
           I LG++PGAGGTQRL R++GKA A  M LS   ++A +A R GLVS V       +  ++
Sbjct: 130 ITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPALTDEYALS 189

Query: 193 LATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKRA 252
           LA T+A  S  AL A K+SL  + E +L  G+  ER+      A+ D REGI AFL KR 
Sbjct: 190 LAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATEDRREGIDAFLHKRT 249

Query: 253 PCFSHR 258
             F  R
Sbjct: 250 AEFKGR 255


Lambda     K      H
   0.321    0.135    0.389 

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: 110
Number of extensions: 3
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: 258
Length of database: 255
Length adjustment: 24
Effective length of query: 234
Effective length of database: 231
Effective search space:    54054
Effective search space used:    54054
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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