Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate WP_084517385.1 H567_RS0115475 hypothetical protein
Query= CharProtDB::CH_091794 (261 letters) >NCBI__GCF_000422285.1:WP_084517385.1 Length = 287 Score = 177 bits (448), Expect = 3e-49 Identities = 105/252 (41%), Positives = 149/252 (59%), Gaps = 3/252 (1%) Query: 3 LNNVILEKE-GKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKS 61 L NV +E V V+TI+RP +NALN + + E+ + D V +++TGAG K Sbjct: 31 LMNVNIENPVSGVRVLTIDRPP-VNALNEEIVDELRDAVKAAMLDGRVRVLVITGAG-KI 88 Query: 62 FVAGADISEMKEMNTIEGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDI 121 FVAGAD+ + + GRK + R + KPVIAA+NG A GGG E+AM+CD+ Sbjct: 89 FVAGADLDRLLAADMDAGRKMADGVKGLHREMRQGGKPVIAAINGMAAGGGLELAMACDV 148 Query: 122 RIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNK 181 RIA NAR G PEV LG+ PG GGTQ L RLVG G A +++FT I A++AL++GLV + Sbjct: 149 RIADQNARMGLPEVTLGVLPGAGGTQMLPRLVGAGKAMEMMFTGMIIDANDALQLGLVEQ 208 Query: 182 VVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTED 241 V ++ A ++A ++V NAP+A+ K A+ M +D LA E+ F T D Sbjct: 209 VAIVESALDLALKMAARMVKNAPLAISEIKAAVYDTMSLPLDQGLAEETGRFARLCRTAD 268 Query: 242 QKDAMTAFIEKR 253 + + +TAF +R Sbjct: 269 KNEGITAFKSRR 280 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: 197 Number of extensions: 7 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: 287 Length adjustment: 25 Effective length of query: 236 Effective length of database: 262 Effective search space: 61832 Effective search space used: 61832 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