Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Echvi_4069 Echvi_4069 Enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::A4YI89 (259 letters) >FitnessBrowser__Cola:Echvi_4069 Length = 261 Score = 214 bits (544), Expect = 2e-60 Identities = 114/260 (43%), Positives = 168/260 (64%), Gaps = 3/260 (1%) Query: 2 EFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KA 60 E I ++ + + ++T+NR KLNA+N LEEL ++ + IR +++TG G KA Sbjct: 3 ESTNILSENKDGILYLTINRESKLNAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGEKA 62 Query: 61 FCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDI 120 F AGADI++ +L A KFS+ G+E+ IE+ KP IA++NG+ALGGG EL++AC + Sbjct: 63 FVAGADISEIAELNELNARKFSENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMACHM 122 Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180 RIA A+ G PE+NLGI PGYGGTQRLT +IG+ +A E++MTGD + +A+ GLVN Sbjct: 123 RIATSNAKFGQPEVNLGIIPGYGGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLVNY 182 Query: 181 VVPL-ANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239 V A Q+ ++ +KI K+P+S+ +I + VN + S +G +E+ + +E Sbjct: 183 VTQTKAEAIQKAEEILQKIMTKAPLSIGMIIDCVN-AVYSNDENGYLIEANSFARCVKSE 241 Query: 240 DKKEGVSAFLEKREPTFKGK 259 D EG SAFLEKR+P FKG+ Sbjct: 242 DYSEGTSAFLEKRKPNFKGE 261 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: 148 Number of extensions: 9 Number of successful extensions: 4 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: 261 Length adjustment: 24 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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 17 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