Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_090271818.1 BLU11_RS02050 enoyl-CoA hydratase
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_900105005.1:WP_090271818.1 Length = 271 Score = 173 bits (438), Expect = 4e-48 Identities = 94/250 (37%), Positives = 146/250 (58%), Gaps = 1/250 (0%) Query: 4 NNVILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFV 63 + ++++K G A++TI+ P A N ++DTL + +IG + +D ++ A+++ G G++ F Sbjct: 16 DKLVVQKAGHTALLTIDNPPA-NTWDTDTLHGLYELIGHLSDDPDIYALVIIGRGDRFFS 74 Query: 64 AGADISEMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRI 123 AGAD+ E + R L F L IAA+NG+A+GGG E A++CDIRI Sbjct: 75 AGADLKMFAEGDKAHARLVARLFGHAFEALRDFSGVTIAALNGYAMGGGLECALACDIRI 134 Query: 124 ASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVV 183 A + G PE G+G+ P GGTQ L+ LVG G AK++I + + +A RIGLV +VV Sbjct: 135 AERQVQLGLPEAGVGLLPCAGGTQALAWLVGEGWAKRMILCGERVDGVKAERIGLVEEVV 194 Query: 184 EPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQK 243 E + + TA +A ++ +P AVK KQ I ++T LA E E F + F ED + Sbjct: 195 EEGQALATALRLAAQVSRQSPQAVKACKQLIQGARSQPMNTLLAAERERFVDLFDLEDTR 254 Query: 244 DAMTAFIEKR 253 + + AF++KR Sbjct: 255 EGVDAFLQKR 264 Lambda K H 0.317 0.134 0.365 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: 152 Number of extensions: 6 Number of successful extensions: 1 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: 261 Length of database: 271 Length adjustment: 25 Effective length of query: 236 Effective length of database: 246 Effective search space: 58056 Effective search space used: 58056 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 (21.6 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