Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate AZOBR_RS07775 AZOBR_RS07775 enoyl-CoA hydratase
Query= BRENDA::Q5SLK3 (254 letters) >FitnessBrowser__azobra:AZOBR_RS07775 Length = 268 Score = 146 bits (369), Expect = 4e-40 Identities = 97/257 (37%), Positives = 141/257 (54%), Gaps = 5/257 (1%) Query: 1 MVLKERQDGVLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAG 60 +VL+E +DGV LTLNRP+ NA++ L+ AL A L +D VRA++L GAG AF AG Sbjct: 14 LVLREDRDGVATLTLNRPQARNALSVGLMGALQAELDTIHQDSTVRAVVLAGAGPAFCAG 73 Query: 61 QDLTEFGDRKPD---YEAHLRRYNRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRL 117 DL E PD YE+ + ++++ +S + +P++ V+G+A AG L DL Sbjct: 74 HDLKEMR-ANPDRAAYESLFVQCSKLMLTVSRIRQPVIAKVHGIATAAGCQLVATCDLAY 132 Query: 118 AAVGASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVV 177 A A F T V IGL + + L R VG A E+LLL + AEEA+ +GLV+R V Sbjct: 133 CADTARFATPGVNIGLFCSTPM-VALSRAVGRKAAMEMLLLGDLIGAEEAVRIGLVNRAV 191 Query: 178 PAEKLMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHE 237 PA++L A ++A A+ K+ L + EA A A + + +D E Sbjct: 192 PADRLDAVVTEAAGKIAAKSPLTLAIGKEAFYRQIELDVEEAYAYAARVMTENMLARDAE 251 Query: 238 EGVRAFREKRPPRFQGR 254 EG+ AF +KRPP + G+ Sbjct: 252 EGIDAFLQKRPPVWCGQ 268 Lambda K H 0.318 0.135 0.371 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: 160 Number of extensions: 9 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: 254 Length of database: 268 Length adjustment: 25 Effective length of query: 229 Effective length of database: 243 Effective search space: 55647 Effective search space used: 55647 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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