Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate H281DRAFT_05322 H281DRAFT_05322 gluconolactonase (EC 3.1.1.17)
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__Burk376:H281DRAFT_05322 Length = 317 Score = 321 bits (822), Expect = 2e-92 Identities = 172/309 (55%), Positives = 199/309 (64%), Gaps = 23/309 (7%) Query: 7 PAVERI---GNMQCGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGC 63 P VER+ G VGESPVW EQALYW DIP + + R +G+ + W LPE C Sbjct: 7 PRVERVEAAGQAPALVGESPVWRVAEQALYWVDIPAQKIVRLVVETGKRSEWLLPEKVAC 66 Query: 64 IAMAPNGWAMA-METGIFL-------------APPPSPGIELGPLQRLATVAHARPDMRF 109 IA G +A ET +F A S +E+ ++LA DMRF Sbjct: 67 IAFDRRGTVLAGCETALFAVTLSGSSTDATAQAVRASEPVEVTG-RKLAAPVFPFDDMRF 125 Query: 110 NDGRCDRQGRFWAGTMVLDTSLGLPLGKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPE 169 NDGRCDRQGRFWAGTMV D SL P G LYR DA + V+D LI NGL +SP+ Sbjct: 126 NDGRCDRQGRFWAGTMVQDMSLANPAGALYRFDAQGVLSA---PVVDGLITQNGLGWSPD 182 Query: 170 GKTMYLSDSHASRQTVWAFDYDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGN 229 GKTMYLSDSH R+ +WAFDY+++TG P+NRRVF D+N Y GRPDGAAVDADGCYWIC N Sbjct: 183 GKTMYLSDSHPLRRQIWAFDYEVETGEPNNRRVFADLNHYVGRPDGAAVDADGCYWICAN 242 Query: 230 DAGFVHRFTPDGRLDRSIAIPTSKPAMCAFGGPGLDTLFVTSIR--IGDDPLSGATFAVR 287 DAG + RFTP G+LDR IA+P KPAMCAFGG LDTLFVTSIR G G FAVR Sbjct: 243 DAGALLRFTPQGKLDRQIAVPAIKPAMCAFGGRDLDTLFVTSIRPGAGASEHDGHLFAVR 302 Query: 288 PGVTGLPEP 296 PGV+GLPEP Sbjct: 303 PGVSGLPEP 311 Lambda K H 0.322 0.140 0.466 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: 418 Number of extensions: 13 Number of successful extensions: 4 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: 300 Length of database: 317 Length adjustment: 27 Effective length of query: 273 Effective length of database: 290 Effective search space: 79170 Effective search space used: 79170 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 (21.9 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