Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_108402835.1 B9Z44_RS06720 enoyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_003063475.1:WP_108402835.1 Length = 268 Score = 167 bits (422), Expect = 3e-46 Identities = 97/264 (36%), Positives = 155/264 (58%), Gaps = 11/264 (4%) Query: 3 FETIE-TKKEGNLFWITLNRPDKLNALNAKL-LEELDRAVSQAESDPEIRVIIITGKG-K 59 + T+E T+ ++ + LNRP+ NALN ++ ++ LD V + ++R +++TG G K Sbjct: 9 YTTLECTQVSDHVLQVCLNRPEVGNALNTQMGVDLLDLWVRLTDVPGDLRCVVLTGAGAK 68 Query: 60 AFCAGADITQFNQLTPAEAWKFSKKGREIMDKIE----ALSKPTIAMINGYALGGGLELA 115 FC G D+ + N +TP +AW++ EI +++ L P I ING+A GGGLE+A Sbjct: 69 IFCGGGDLKERNGMTP-QAWQYQ---HEIFERLYWALIDLPLPVIGAINGHAYGGGLEMA 124 Query: 116 LACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKY 175 L CD A+++A+ LPE+ LGI PG GGTQ L R +G+ RA E+ +TG + A + Sbjct: 125 LCCDFLYASQDARFALPEVTLGIMPGMGGTQNLPRALGERRAKELALTGRPFSAEQALAW 184 Query: 176 GLVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVV 235 GLVN+V + + A++IA +P+S+ IK+ + G L + E + + Sbjct: 185 GLVNQVAAPDAVLALALETAQRIAANAPLSVRQIKKSIRYGGQMELRTAYRFEVEAYNRL 244 Query: 236 FSTEDKKEGVSAFLEKREPTFKGK 259 T+D++EGV+AF +KR P FKG+ Sbjct: 245 VDTDDRREGVAAFNDKRPPVFKGR 268 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: 172 Number of extensions: 13 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: 268 Length adjustment: 25 Effective length of query: 234 Effective length of database: 243 Effective search space: 56862 Effective search space used: 56862 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 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