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.
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:
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