Align Gluconolactonase (characterized, see rationale)
to candidate WP_051242121.1 H537_RS0107640 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:A0A165IRV8 (316 letters) >NCBI__GCF_000430725.1:WP_051242121.1 Length = 301 Score = 151 bits (381), Expect = 2e-41 Identities = 109/300 (36%), Positives = 140/300 (46%), Gaps = 15/300 (5%) Query: 24 AVRCVIALGNALGEGVLWSVREQAVYWVDILGRELHRWDPATGAHQRWTFDEEISAIAER 83 AV + + N +GE +WSV EQA+YWVDI GR LHR+D AT + W E + IA Sbjct: 10 AVEALCPVRNRVGESPVWSVAEQALYWVDIEGRALHRFDWATRQERHWALAERVGCIALH 69 Query: 84 AHAPGFIVTLRRGFALFDPAT--DMAPRYLHQPEPDRAGNRFNDGKCDAQGRFWAGS--M 139 A G I + G P D+ L + + G RFNDG+CD QGRFW S M Sbjct: 70 A-GGGLIAGMETGVFRLQPGAGDDIRVELLQGVQFAQPGMRFNDGRCDRQGRFWLSSMVM 128 Query: 140 DFACEAPTGALYRYDSDGSCTRHDDGFAVTNGPTWSGTGQGAAMFFNATIEGNTYRYDSD 199 D + P G LYRYD+ G DG NG +S G+ + + + +D D Sbjct: 129 DMSLAQPAGVLYRYDARGLVPML-DGLITGNGLGFSPDGRTLYLSDSHPKVQRVWAFDLD 187 Query: 200 LATGTVSNKTLWKHWLPEDGLPDGMTTDAQGRLWIAHWGGWCVTCHDPVTAAELGRVRLP 259 A G +SN+ + G PDG D G WI V P E +RLP Sbjct: 188 -AQGNLSNRREFIDMNQYPGRPDGAAVDEDGAYWICGNDAGQVHRFGPDGRLERS-LRLP 245 Query: 260 VSQVTTCAFGGADLRTLFISSARVGLTPEQLAA---EPLAGALFAVDTDSLGLPAHPFGG 316 +S+ C+FGG LR LFI+S + P Q AA L GA+ GLP PF G Sbjct: 246 LSKPAMCSFGGPALRHLFITS----IPPAQPAAGFDAALDGAVLVAQPGPRGLPEMPFAG 301 Lambda K H 0.321 0.137 0.457 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: 406 Number of extensions: 26 Number of successful extensions: 6 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: 316 Length of database: 301 Length adjustment: 27 Effective length of query: 289 Effective length of database: 274 Effective search space: 79186 Effective search space used: 79186 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 24 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