Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_012277951.1 SHAL_RS14880 enoyl-CoA hydratase
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_000019185.1:WP_012277951.1 Length = 269 Score = 164 bits (415), Expect = 2e-45 Identities = 87/243 (35%), Positives = 133/243 (54%), Gaps = 1/243 (0%) Query: 12 GKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAGADISEM 71 G AV+++N P A N + +L+E+ + + + EV A+++T G+K F AGAD+ Sbjct: 22 GHTAVISMNNPPA-NTWTAQSLQELKQKVLALNENKEVYALVITAEGDKFFSAGADLKLF 80 Query: 72 KEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDIRIASSNARFG 131 + + + F L IAA+NG+A+GGG E+A++CD+RI A+ Sbjct: 81 ADGDKQNAADMARYFGEAFETLSTFHGVSIAAINGYAMGGGLEVALACDLRICEEQAQMA 140 Query: 132 QPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNKVVEPSELMNT 191 PE +G+ P GGTQ L+ LVG G AK++I + I A++A +IGLV +VV N Sbjct: 141 LPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERINAEKAEKIGLVEEVVVQGNAFNA 200 Query: 192 AKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTEDQKDAMTAFIE 251 A +A K+ + +P +VK KQ + G L E E F F TEDQ + ++AF+ Sbjct: 201 AMALAEKVANQSPSSVKACKQLVQAGRSMPRSQVLPLEREYFANLFDTEDQAEGVSAFLN 260 Query: 252 KRK 254 KRK Sbjct: 261 KRK 263 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: 151 Number of extensions: 8 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: 261 Length of database: 269 Length adjustment: 25 Effective length of query: 236 Effective length of database: 244 Effective search space: 57584 Effective search space used: 57584 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