Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_007155006.1 MDG893_RS16745 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000170835.1:WP_007155006.1 Length = 263 Score = 169 bits (428), Expect = 5e-47 Identities = 96/247 (38%), Positives = 135/247 (54%), Gaps = 4/247 (1%) Query: 17 ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFN----Q 72 +TLNRPD LN+ N ++ E++ +A+SQ D +RV++ITG G+ FCAG D++ + Q Sbjct: 17 LTLNRPDNLNSFNVEMHEQMRKAISQVRKDSSVRVLVITGAGRGFCAGQDLSDRSVAPDQ 76 Query: 73 LTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLP 132 P K +M + L P + +NG A G G +ALACDI +AA A Sbjct: 77 DAPDLGESLEKYYNPMMRSLRDLPMPVLCAVNGVAAGAGANIALACDITLAARSASFVQA 136 Query: 133 EINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETR 192 LG+ P GGT L R+ G RA M + GD+I + AE +G++ R V L +ET Sbjct: 137 FCKLGLIPDSGGTWTLPRIAGMARAKGMALLGDKIRAEQAENWGMIWRCVDDETLMEETM 196 Query: 193 KLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKR 252 KLA A + LALIK ++ + L LE + +ED +EGV+AF+EKR Sbjct: 197 KLARHFATQPTKGLALIKRALHASSSNTFEEQLNLERDLQRMAGRSEDYREGVAAFMEKR 256 Query: 253 EPTFKGK 259 PTFKGK Sbjct: 257 TPTFKGK 263 Lambda K H 0.315 0.135 0.382 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: 151 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: 259 Length of database: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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: 42 (22.0 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