Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_025763144.1 X939_RS0110100 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >NCBI__GCF_000566685.1:WP_025763144.1 Length = 275 Score = 103 bits (257), Expect = 4e-27 Identities = 77/246 (31%), Positives = 116/246 (47%), Gaps = 8/246 (3%) Query: 17 ITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAE--RD 74 I L RPE NA + +E+A LA A E R ++L+ F AGAD+ + D Sbjct: 31 IVLNRPEKRNAFTLTMAEEIAYALAYAHYSKEVRCLLLSARGPVFCAGADLNAFHDPASD 90 Query: 75 LVGILEDPRVAHWQRI----AAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQP 130 LV PR + R+ A KP IA V G L GG + +I+ +A++ P Sbjct: 91 LVNPTL-PRPSETVRLGDAFAGLLKPSIAQVEGAVLAGGFLMICGCTFVISVPEAQYSLP 149 Query: 131 EINLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERAL 190 E+ GI P G+ + M+M ++G+A A A GL+++V + A Sbjct: 150 EVKRGIWPMQVMASLDGLISGRKI-MEMAITGRAYSAAEALEMGLITQVVTHTEIQDTAE 208 Query: 191 AIARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKR 250 +A++I +APLA++ A + A + L +AD EG+RAF+EKR Sbjct: 209 ELAKLITSQAPLAIQEGMRAYADLHEMPSAERQGMLQQRLNTLLLSADAKEGVRAFREKR 268 Query: 251 RPEFTG 256 RPE+ G Sbjct: 269 RPEWKG 274 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: 183 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 257 Length of database: 275 Length adjustment: 25 Effective length of query: 232 Effective length of database: 250 Effective search space: 58000 Effective search space used: 58000 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