Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate Echvi_4069 Echvi_4069 Enoyl-CoA hydratase/carnithine racemase
Query= SwissProt::Q0AVM1 (260 letters) >FitnessBrowser__Cola:Echvi_4069 Length = 261 Score = 233 bits (593), Expect = 4e-66 Identities = 123/254 (48%), Positives = 172/254 (67%), Gaps = 2/254 (0%) Query: 5 NIILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVA 64 NI+ E ++ + L INR +NA+N DTL E+K+ V+D+ ++ +++TGSG+K+FVA Sbjct: 6 NILSENKDGILYLTINRESKLNAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGEKAFVA 65 Query: 65 GADIAFMQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDFRIA 124 GADI+ + L+ + AR+F GQ+VF LIE+ KPVIA VNGFALGGGCEL+M C RIA Sbjct: 66 GADISEIAELNELNARKFSENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMACHMRIA 125 Query: 125 ASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVVQ 184 SNAKFGQPEV LGI PG+GGTQRL L+G A +LL T D+++A EA +GLVN V Q Sbjct: 126 TSNAKFGQPEVNLGIIPGYGGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLVNYVTQ 185 Query: 185 PE-ELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFATQDQK 243 + E + + ++I +I++K L++ + N D + IEA++F C ++D Sbjct: 186 TKAEAIQKAEEILQKIMTKAPLSIGMIIDCVNAVYSND-ENGYLIEANSFARCVKSEDYS 244 Query: 244 EGMTAFLEKRKANF 257 EG +AFLEKRK NF Sbjct: 245 EGTSAFLEKRKPNF 258 Lambda K H 0.319 0.136 0.378 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: 182 Number of extensions: 3 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: 260 Length of database: 261 Length adjustment: 25 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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