Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate 3607183 Dshi_0604 amidohydrolase 2 (RefSeq)
Query= BRENDA::A9CEQ7 (292 letters) >FitnessBrowser__Dino:3607183 Length = 286 Score = 144 bits (363), Expect = 2e-39 Identities = 86/274 (31%), Positives = 131/274 (47%), Gaps = 6/274 (2%) Query: 13 PNPAFPRGAVDTQMHMYLP--GYPALPGGPGLPPGALPGPEDYRRLMQWLGIDRVIITQG 70 P P GA D H+ +P +P + PP A Y+ L LGI+R +I Q Sbjct: 15 PKRPLPPGATDCHSHVIVPEADHPFVANRSYTPPPATLA--QYKALHARLGIERAVIVQP 72 Query: 71 NAHQRDNGNTLACVAEMGEAAHAVVIIDATTTEKDMEKLTAAGTVGARIMDLPGGAVNLS 130 + + DN TL +A G + ++DA + +D++ + AAG GARI L G + L Sbjct: 73 SVYGTDNSVTLEAIAGYGPGCRGIAVVDADVSMRDLQAMNAAGIRGARINMLFSGGIGLD 132 Query: 131 ELDAVDERAHAADWMVAVQFDGNGLLDHLPRLQKIRSRWVFDHHGKFFKGIRTDGPEMAA 190 +L+ + R DW + DG L D RL + V DH G D P A Sbjct: 133 DLEPLARRIADLDWHFQLLIDGPTLADLEARLANLPVPVVIDHMGHMQTHDGLDQPGFRA 192 Query: 191 LLKLIDRGNLWFKFAGVYESSRKSWPYADVAAFSRVIAAHAPERIVWGTNWPHNSVRETA 250 L +L+ RGN W K +G Y S + + DV F++ + + E +VWGT+WPH ++ + Sbjct: 193 LRRLVVRGNTWVKLSGNYRMSSQRPRFEDVVPFAQALISDNSEHMVWGTDWPHPAMLD-- 250 Query: 251 AYPDDARLAELTLGWLPDEAARHRALVENPEALF 284 PDD L + ++ + + R LV+NP L+ Sbjct: 251 FMPDDGSLVDALDAYVTSQDQKQRILVDNPATLY 284 Lambda K H 0.319 0.136 0.426 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: 236 Number of extensions: 12 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: 292 Length of database: 286 Length adjustment: 26 Effective length of query: 266 Effective length of database: 260 Effective search space: 69160 Effective search space used: 69160 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: 48 (23.1 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