Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Pf6N2E2_1834 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1834 Length = 256 Score = 210 bits (535), Expect = 2e-59 Identities = 114/251 (45%), Positives = 160/251 (63%) Query: 4 LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63 ++V R V +L LNR RNAL+ ++ + + + ++ D+ ++V VITG FAAGA Sbjct: 5 VVVERNGAVAILRLNRVEKRNALDLSMRVAIASAMQELERDSGVAVIVITGGDSVFAAGA 64 Query: 64 DLNEMAEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENA 123 DLN + +K Q WA + KPLIAAV+G+ALGAGCELA++CD++VA +A Sbjct: 65 DLNLLVDKGAQQVAELDLGQYWAPVAKSQKPLIAAVSGFALGAGCELAMMCDILVADNSA 124 Query: 124 RFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPSDLT 183 RFG PE +GIMPGAGGTQRL+R+VGK +AS M+L+GE ++A++A Q GLVS++ Sbjct: 125 RFGQPEARVGIMPGAGGTQRLLRAVGKPVASLMLLAGELLSAERASQLGLVSELVTEGSA 184 Query: 184 LEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHEGISA 243 L A+ LA A P AL+A K+ L + +L LA E + F LL T+D+ EG+ A Sbjct: 185 LARAIVLAQATATMPPKALRAIKRVLALGADQSLDLALALENREFLLLFDTQDKTEGMRA 244 Query: 244 FLQKRTPDFKG 254 FL KR P + G Sbjct: 245 FLDKRPPRYTG 255 Lambda K H 0.318 0.130 0.356 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: 103 Number of extensions: 1 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: 255 Length of database: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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 (21.8 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