Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase
Query= metacyc::MONOMER-15953 (257 letters) >FitnessBrowser__azobra:AZOBR_RS18155 Length = 248 Score = 164 bits (415), Expect = 2e-45 Identities = 101/242 (41%), Positives = 134/242 (55%), Gaps = 2/242 (0%) Query: 14 VRLITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSR-KAFAAGADIKEMAE 72 V ITL RP+ LNA+ ++ +L A +A D + R VVLTG+ +AF G+DI+E+ Sbjct: 5 VATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDIRELDR 64 Query: 73 RDLVGILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEI 132 D + R + I KP IAAVNG+ GGG E AM DI IA E+A+FG PEI Sbjct: 65 YDTAWNFRN-REDYCDAIRGLRKPSIAAVNGYAFGGGLETAMSCDIRIASENAQFGAPEI 123 Query: 133 NLGIMPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERALAI 192 LG + G G L ++G S A M+L+G I A A GLVSEV + + RA I Sbjct: 124 KLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPADRLLARAQEI 183 Query: 193 ARVIAQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKRRP 252 A ++A +AP+A AK L A + + +ER T+ TAD AEG AF+EKR P Sbjct: 184 AAIVASRAPIAAETAKLNLKAAHTMPVEKAIEYERDLQTICFATADAAEGRAAFKEKRSP 243 Query: 253 EF 254 F Sbjct: 244 VF 245 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: 178 Number of extensions: 9 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: 248 Length adjustment: 24 Effective length of query: 233 Effective length of database: 224 Effective search space: 52192 Effective search space used: 52192 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: 46 (22.3 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