Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30355 Length = 264 Score = 135 bits (339), Expect = 1e-36 Identities = 81/265 (30%), Positives = 138/265 (52%), Gaps = 8/265 (3%) Query: 1 MPEFKVDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAF 60 M + +V G + + ++ ++NA+S +ML L + + D+ VITGAGD AF Sbjct: 1 MSDLEVSTVGRVMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGD-AF 59 Query: 61 CAGADLKERATMAEDEVRAFLDGLRRTFR-------AIEKSDCVFIAAINGAALGGGTEL 113 C+G DL RA + + L+ R + AIE + IAA+NGAA+G G +L Sbjct: 60 CSGGDLGRRAAESAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDL 119 Query: 114 ALACDLRVAAPAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFS 173 +L CD+R A+ +A +++G+IPG GG L R+VG +A +L+ T ++A EA + Sbjct: 120 SLQCDMRFASESARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALA 179 Query: 174 VGLANRLAPEGHLLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEE 233 +G+ NR+ + L+ A + + PI + K + + +L +L + Sbjct: 180 LGIVNRVFSDDELMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAV 239 Query: 234 ILKTEDRLEGLRAFAEKRAPVYKGR 258 + T+D E ++A+ EKR P + G+ Sbjct: 240 VQSTDDYKEAIKAYKEKRKPRFIGK 264 Lambda K H 0.319 0.136 0.380 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: 124 Number of extensions: 5 Number of successful extensions: 3 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: 264 Length adjustment: 25 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 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 Apr 09 2024. 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