Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate CCNA_02658 CCNA_02658 3-hydroxybutyryl-CoA dehydratase
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Caulo:CCNA_02658 Length = 265 Score = 142 bits (357), Expect = 9e-39 Identities = 92/261 (35%), Positives = 138/261 (52%), Gaps = 13/261 (4%) Query: 7 DARGPIEIWTIDGESRRNAISR-AMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGAD 65 + RG I I T++ NA+ ++ ++ +D+R V++TGAG KAF AG D Sbjct: 7 EKRGHIAILTLNRPDAMNALGAPGDGDQVAAACEAINDDQDIRCVILTGAG-KAFSAGGD 65 Query: 66 LKERATMAED--------EVR-AFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALA 116 +K A A + +VR + + R RAI + IAA+NGAA+G G ++A Sbjct: 66 VK--AMKAREGAFGGNGVKVRDGYRKNIHRIVRAIYGLEVPSIAAVNGAAIGLGCDVACM 123 Query: 117 CDLRVAAPAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGL 176 D+R+AA A G+T +KLG+IPG GG + R +G RA +L+ T I+AA+A GL Sbjct: 124 TDIRIAADTARFGVTFLKLGLIPGDGGAWLMPRTIGMSRAAELLFTGDVIDAAKAAEWGL 183 Query: 177 ANRLAPEGHLLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILK 236 ++ P G L+ A LAE + + P A+ AK + G D + + Sbjct: 184 ISKAVPAGDLMGEALALAERIAQQPPHALRMAKSLLKHGQTASYDTLMEMSAAAQAIAHH 243 Query: 237 TEDRLEGLRAFAEKRAPVYKG 257 TED +EG+ A EKR+PV+KG Sbjct: 244 TEDHMEGVDAILEKRSPVFKG 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: 177 Number of extensions: 8 Number of successful extensions: 1 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: 265 Length adjustment: 25 Effective length of query: 233 Effective length of database: 240 Effective search space: 55920 Effective search space used: 55920 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