Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_057507300.1 ABB28_RS03505 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_001431535.1:WP_057507300.1 Length = 687 Score = 115 bits (287), Expect = 3e-30 Identities = 70/189 (37%), Positives = 105/189 (55%), Gaps = 6/189 (3%) Query: 11 EQGVRLITLQRPEA-LNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKE 69 + GV ++ L R +A +NA++ +L EL + D V+ + + F AGAD+KE Sbjct: 19 DDGVVVLNLDRQDANVNAMSQDVLLELGDLIERIAIDPPKGVVIQSAKKAGFIAGADLKE 78 Query: 70 MAERDLVGILEDP---RVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDA- 125 E D G + D +Q++A P +AA++G CLGGG ELA+ +A D+ Sbjct: 79 FQEFDRRGTVNDAIRRGQVTYQKLAELPCPTVAAIHGHCLGGGTELALACRYRVASNDSS 138 Query: 126 -RFGQPEINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPEL 184 R G PE LGI PG GG+ RL + VG AM M+L+G+ + A A+ GLV +V P L Sbjct: 139 TRIGLPETQLGIFPGWGGSARLPQLVGAPAAMDMMLTGRTLSASAARNIGLVDKVVAPAL 198 Query: 185 TIERALAIA 193 ++ A+A+A Sbjct: 199 LLDTAVALA 207 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: 409 Number of extensions: 16 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: 257 Length of database: 687 Length adjustment: 31 Effective length of query: 226 Effective length of database: 656 Effective search space: 148256 Effective search space used: 148256 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: 50 (23.9 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