Align gluconolactonase (EC 3.1.1.17) (characterized)
to candidate H281DRAFT_05322 H281DRAFT_05322 gluconolactonase (EC 3.1.1.17)
Query= BRENDA::Q64374 (299 letters) >FitnessBrowser__Burk376:H281DRAFT_05322 Length = 317 Score = 128 bits (322), Expect = 1e-34 Identities = 91/303 (30%), Positives = 140/303 (46%), Gaps = 30/303 (9%) Query: 17 GESPVWEEASQSLLFVDIPSKIICRWDTVSNQVQRVAVDAPVSSVALRQLGGYVATIGTK 76 GESPVW A Q+L +VDIP++ I R + + + V+ +A + G +A T Sbjct: 23 GESPVWRVAEQALYWVDIPAQKIVRLVVETGKRSEWLLPEKVACIAFDRRGTVLAGCETA 82 Query: 77 FCALNWENQSVFVLAMVDEDKK-----------------NNRFNDGKVDPAGRYFAGTMA 119 A+ S A + + RFNDG+ D GR++AGTM Sbjct: 83 LFAVTLSGSSTDATAQAVRASEPVEVTGRKLAAPVFPFDDMRFNDGRCDRQGRFWAGTMV 142 Query: 120 EETAPAVLERHQGSLYSLFPDHSVKK-YFDQVDISNGLDWSLDHKIFYYIDS--LSYTVD 176 ++ + L G+LY + D + NGL WS D K Y DS L + Sbjct: 143 QDMS---LANPAGALYRFDAQGVLSAPVVDGLITQNGLGWSPDGKTMYLSDSHPLRRQIW 199 Query: 177 AFDYDLQTGQISNRRIVYKMEKDEQIPDGMCIDAEGKLWVACYNGGRVIRLDPETGKRLQ 236 AFDY+++TG+ +NRR+ + PDG +DA+G W+ + G ++R P+ GK + Sbjct: 200 AFDYEVETGEPNNRRVFADLNHYVGRPDGAAVDADGCYWICANDAGALLRFTPQ-GKLDR 258 Query: 237 TVKLPVDKTTSCCFGGKDYSEMYVTCARDGLNAEGLLRQPDAGNIFKITGLGVKGIAPYS 296 + +P K C FGG+D ++VT R G A G++F + GV G+ Sbjct: 259 QIAVPAIKPAMCAFGGRDLDTLFVTSIRPGAGA-----SEHDGHLFAVRP-GVSGLPEPE 312 Query: 297 YAG 299 +AG Sbjct: 313 FAG 315 Lambda K H 0.319 0.137 0.419 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: 284 Number of extensions: 20 Number of successful extensions: 5 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: 299 Length of database: 317 Length adjustment: 27 Effective length of query: 272 Effective length of database: 290 Effective search space: 78880 Effective search space used: 78880 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