GapMind for catabolism of small carbon sources

 

Aligments for a candidate for badK in Herbaspirillum seropedicae SmR1

Align BadK (characterized)
to candidate HSERO_RS20665 HSERO_RS20665 2,3-dehydroadipyl-CoA hydratase

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS20665 HSERO_RS20665
           2,3-dehydroadipyl-CoA hydratase
          Length = 262

 Score =  196 bits (498), Expect = 4e-55
 Identities = 114/244 (46%), Positives = 149/244 (61%), Gaps = 5/244 (2%)

Query: 17  ITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAAWSYS 76
           +TLNRP + NAL +  +  +  AL   + DD +  +VI+GN +AFAAGAD+  M    + 
Sbjct: 22  LTLNRPALRNALRNQSLREIVAALARAEEDDSVRVVVISGNEKAFAAGADLNEMI---HK 78

Query: 77  DVYGSNFITRN--WETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALPEIK 134
           D   +    R   W  I +  KP+LAAV G A G GCEL +  DI IA R AK   PEI 
Sbjct: 79  DAIATQLDVRAQYWRAIARFPKPILAAVNGYALGAGCELLMHADIAIAARGAKIGQPEIN 138

Query: 135 LGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETVALA 194
           +G LPGAGGTQRL R +GK  AM M LS   ++A++A + GLV+ VVDDD   + T+ALA
Sbjct: 139 VGTLPGAGGTQRLIRTVGKPLAMKMVLSGEFISADQALQAGLVAEVVDDDATLERTLALA 198

Query: 195 TTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKRAPC 254
            +IA  S  A+   KE++ ++FE  L  G+LFER+      ASAD +EGI AF EKRA  
Sbjct: 199 HSIAQKSPLAVRLAKEAMLQSFELGLEAGLLFERKSFSLMAASADRQEGIAAFQEKRAAV 258

Query: 255 FSHR 258
           FS R
Sbjct: 259 FSGR 262


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: 118
Number of extensions: 5
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: 262
Length adjustment: 24
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
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.

Links

Downloads

Related tools

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