GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Sinorhizobium meliloti 1021

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

Query= metacyc::MONOMER-892
         (260 letters)



>FitnessBrowser__Smeli:SMc01669
          Length = 263

 Score =  114 bits (285), Expect = 2e-30
 Identities = 81/260 (31%), Positives = 125/260 (48%), Gaps = 10/260 (3%)

Query: 4   EDLIYEIRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFC 63
           + ++ EI  G+A + +NRP+K+NA      D L+  L +   D+ V A++L GAGDRAF 
Sbjct: 3   DTVLIEISAGIALLTLNRPEKLNALNYELIDRLLALLDRIEIDETVQAVILTGAGDRAFS 62

Query: 64  TGGDQSTHDGNYDGRGTVGLPME------ELHTAIRDVPKPVIARVQGYAIGGGNVLATI 117
            GGD     G+   +G      +      +L   +   PKPVIA V G A GGG  +   
Sbjct: 63  AGGDIHEFSGSV-AKGVNAATRDFVRRGQQLTHRLEAFPKPVIAAVNGLAYGGGCEVTEA 121

Query: 118 CDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGL 177
             L I SE+A F +   K+       GT  L R+ G K+A E+      +S + A  MGL
Sbjct: 122 VHLAIASERARFAKPEIKLAMPPTFGGTQRLPRLAGRKRALELLLTGDAFSPQRALDMGL 181

Query: 178 ANLCVPHDELDAEVQKWGEELCERSP--TALAIAKRSFNMDTAHQAGIAGMGMYALKLYY 235
            N  VPH++L A  +         SP  TA  I   +  ++ A   G+        ++  
Sbjct: 182 VNAVVPHEQLIASARALAGRTIRHSPLATAAIITAVTRGLNMAIGEGLLCESEQFARM-V 240

Query: 236 DTDESREGVKALQEKRKPEF 255
            + + +EG+ A +E+R+P +
Sbjct: 241 PSHDLKEGLAAWKERREPRY 260


Lambda     K      H
   0.319    0.138    0.418 

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: 162
Number of extensions: 11
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: 260
Length of database: 263
Length adjustment: 25
Effective length of query: 235
Effective length of database: 238
Effective search space:    55930
Effective search space used:    55930
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 (21.7 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