Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_076579030.1 BB347_RS01645 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_001971705.1:WP_076579030.1 Length = 657 Score = 188 bits (478), Expect = 2e-52 Identities = 103/263 (39%), Positives = 159/263 (60%), Gaps = 5/263 (1%) Query: 1 MEFETIETKKEGNLFW-ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG- 58 +EF+ I + G++ I L+RP ++N ++ LLEEL AV E D E+R I+ITG+G Sbjct: 396 VEFDAIRVEYPGDMVGHIVLDRPHRMNTISDDLLEELATAVDLLEDDEEVRSILITGEGE 455 Query: 59 KAFCAGADITQF--NQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELAL 116 KAF AGAD+ P E + S+ G++ K+EA P +A I+G+ LGGG+EL++ Sbjct: 456 KAFSAGADVQSMAAGGADPLEGQELSRLGQQTFGKLEACDLPIVAGIDGFCLGGGMELSM 515 Query: 117 ACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYG 176 D+R+A+E ++ G PE++LG+ PG+GGTQRL ++G+GRA E+++T +R + YG Sbjct: 516 CADLRVASERSEFGQPELDLGLLPGWGGTQRLKHIVGEGRAKEIILTAERFDAETMADYG 575 Query: 177 LVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVF 236 VN VV LE E LA +A P++ K + G +GL E+ +G + Sbjct: 576 FVNDVVANNELEDEALDLATDLAGGPPVAQKFTKRAMLTGRHD-TEAGLEYEASAFGHLM 634 Query: 237 STEDKKEGVSAFLEKREPTFKGK 259 +T+D EG++AF+ EP F+GK Sbjct: 635 ATDDLMEGITAFMGDGEPEFEGK 657 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: 359 Number of extensions: 18 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: 259 Length of database: 657 Length adjustment: 31 Effective length of query: 228 Effective length of database: 626 Effective search space: 142728 Effective search space used: 142728 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: 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