GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Sinorhizobium meliloti 1021

Align BadK (characterized)
to candidate SMc01669 SMc01669 enoyl-CoA hydratase

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



>FitnessBrowser__Smeli:SMc01669
          Length = 263

 Score =  156 bits (394), Expect = 5e-43
 Identities = 98/265 (36%), Positives = 144/265 (54%), Gaps = 12/265 (4%)

Query: 3   SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAF 61
           S+ +L E    + ++TLNRP+ LNALN  L+D L   L   + D+ + A+++ G   RAF
Sbjct: 2   SDTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAF 61

Query: 62  AAGADIASMAAWSYSDVYGSNFITRNW--------ETIRQIRKPVLAAVAGLAYGGGCEL 113
           +AG DI     +S S   G N  TR++          +    KPV+AAV GLAYGGGCE+
Sbjct: 62  SAGGDIHE---FSGSVAKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEV 118

Query: 114 ALACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADR 173
             A  + IA   A+FA PEIKL + P  GGTQRLPR  G+ +A+++ L+    + + A  
Sbjct: 119 TEAVHLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALD 178

Query: 174 YGLVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHA 233
            GLV+ VV  ++L     ALA      S  A  A+  ++ R     + EG+L E  +   
Sbjct: 179 MGLVNAVVPHEQLIASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFAR 238

Query: 234 RFASADAREGIQAFLEKRAPCFSHR 258
              S D +EG+ A+ E+R P ++ R
Sbjct: 239 MVPSHDLKEGLAAWKERREPRYAGR 263


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: 135
Number of extensions: 6
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: 263
Length adjustment: 25
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
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 (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