Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_046008793.1 OLEAN_RS08010 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000967895.1:WP_046008793.1 Length = 260 Score = 118 bits (295), Expect = 1e-31 Identities = 86/259 (33%), Positives = 124/259 (47%), Gaps = 26/259 (10%) Query: 14 VRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAER 73 + IT RPE N L+ + LA + + D E R V+ + K F++G ++ + A Sbjct: 13 IMTITFNRPEMYNPLDPESYFLLAQAMYRLQHDDELRVAVVQANGKHFSSGLELDKWAPI 72 Query: 74 DLVGILEDPRVAHWQRIA----AFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQ 129 G D H +KP+I AV G C G EL ++ DI IA +ARF Q Sbjct: 73 FANGEYPDLPPEHLDPYGNKGEVLTKPVIMAVQGICYTSGLELLLNTDIRIATPEARFAQ 132 Query: 130 PEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERA 189 E+ GI P GGT RL R +G S A + +L+G A+ A G+V E+ + E A Sbjct: 133 LEVQRGIYPCGGGTVRLPREIGWSNAQRYILTGDEFTAQQALEWGMVQELVERDQLHEHA 192 Query: 190 LAIARVIAQKAPLAVRLA-----------KEALLKAEDTDLASGLRFERHAFTVLAGTAD 238 +IA+ IA+ APL V+ A +EA LK TDL ++ E D Sbjct: 193 RSIAKKIAKAAPLGVQAALRSAKTCRVHGQEAALKTLFTDLPKIMKSE-----------D 241 Query: 239 RAEGIRAFQEKRRPEFTGR 257 EGI +F ++R +FTG+ Sbjct: 242 AKEGIASFLQRREAKFTGK 260 Lambda K H 0.320 0.134 0.374 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: 143 Number of extensions: 5 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: 257 Length of database: 260 Length adjustment: 24 Effective length of query: 233 Effective length of database: 236 Effective search space: 54988 Effective search space used: 54988 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 (21.8 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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