Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate BPHYT_RS24170 BPHYT_RS24170 gluconolactonase
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__BFirm:BPHYT_RS24170 Length = 309 Score = 326 bits (836), Expect = 4e-94 Identities = 172/307 (56%), Positives = 199/307 (64%), Gaps = 15/307 (4%) Query: 1 MHLNVEPAVERI---GNMQCGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPL 57 M P VER+ G VGESPVW A EQALYW DIP + + R SG+ + W L Sbjct: 1 MSAAANPRVERVEAAGQAPAAVGESPVWRAAEQALYWVDIPAQKIVRLRIDSGERSEWLL 60 Query: 58 PEMAGCIAMAPNGWAMA-METGIFLAPPPSPGIELGPLQ----RLATVAHARPDMRFNDG 112 PE CIA G +A ETG+F +Q +LA A DMRFNDG Sbjct: 61 PEKVACIAFDHRGTVLAGCETGLFALTLTESAANGEAVQVTGRKLAAPDFACDDMRFNDG 120 Query: 113 RCDRQGRFWAGTMVLDTSLGLPLGKLYRLDAAAARTGRVDA-VIDDLIVPNGLAFSPEGK 171 RCDRQGRFWAGTMV D + P G LYR D G + A V+++LI NGLA+SP+G Sbjct: 121 RCDRQGRFWAGTMVQDMAAAKPAGALYRFD----ERGMLSAPVVEELITQNGLAWSPDGA 176 Query: 172 TMYLSDSHASRQTVWAFDYDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDA 231 TMYLSDSH R+ +WAFDYDI++G P NRRVF D+N + GRPDGAAVDADGCYWIC NDA Sbjct: 177 TMYLSDSHPLRRQIWAFDYDIESGEPRNRRVFADLNQHAGRPDGAAVDADGCYWICANDA 236 Query: 232 GFVHRFTPDGRLDRSIAIPTSKPAMCAFGGPGLDTLFVTSIR--IGDDPLSGATFAVRPG 289 G + RFTP+G+LDR IA+P KPAMCAFGG LDTLFVTSIR G FAVRPG Sbjct: 237 GLLLRFTPEGKLDRQIAVPAIKPAMCAFGGRELDTLFVTSIRPAANASEHDGHLFAVRPG 296 Query: 290 VTGLPEP 296 +TGLPEP Sbjct: 297 ITGLPEP 303 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: 394 Number of extensions: 9 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: 309 Length adjustment: 27 Effective length of query: 273 Effective length of database: 282 Effective search space: 76986 Effective search space used: 76986 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