Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase
Query= SwissProt::Q0AVM1 (260 letters) >FitnessBrowser__SynE:Synpcc7942_0597 Length = 279 Score = 130 bits (326), Expect = 4e-35 Identities = 95/262 (36%), Positives = 134/262 (51%), Gaps = 8/262 (3%) Query: 3 YENIILEK-EEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKS 61 YE+I EK E +A + INRP NA T++E+ DA +D A+ ++++TG+G + Sbjct: 12 YEDIRYEKCAEGIAKITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGPHT 71 Query: 62 -----FVAGADIAFMQNLSAMEAREFGALGQ-KVFRLIEAMEKPVIAAVNGFALGGGCEL 115 F AG D + ++ L + RLI + K VIA V G+A+GGG L Sbjct: 72 DGRYAFCAGGDQSVRGAGGYIDEEGLPRLNVLDLQRLIRTIPKVVIALVAGYAIGGGHVL 131 Query: 116 AMCCDFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFR 175 + CD IAA NA FGQ +G G G L RLVG A+++ + A EA + Sbjct: 132 HILCDLTIAADNAVFGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQYGAKEALQ 191 Query: 176 IGLVNKVVQPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGL 235 +GLVN VV EEL E + A IL K +A+R KAA N + + + A L Sbjct: 192 MGLVNTVVPVEELEAEGIRWALEILEKSPIAIRCLKAAFNAELD-GMAGIQELAGHATHL 250 Query: 236 CFATQDQKEGMTAFLEKRKANF 257 + T++ EG AFLEKR +F Sbjct: 251 YYLTEEGSEGKQAFLEKRSPDF 272 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: 183 Number of extensions: 8 Number of successful extensions: 3 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: 279 Length adjustment: 25 Effective length of query: 235 Effective length of database: 254 Effective search space: 59690 Effective search space used: 59690 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