Align Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale)
to candidate BPHYT_RS01825 BPHYT_RS01825 sugar ABC transporter substrate-binding protein
Query= uniprot:A0KWY4 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS01825 Length = 339 Score = 204 bits (519), Expect = 2e-57 Identities = 112/267 (41%), Positives = 163/267 (61%), Gaps = 11/267 (4%) Query: 25 VGFSQVGSESGWRTSFSEAVKAEAKQRGIDLKFADAQQKQENQIKAVRSFIAQGVDAIII 84 VGF+Q S + WR + +++ K A + G L DA Q+ +++ IAQ VD ++ Sbjct: 53 VGFAQTESNNPWRLAETKSFKDIAAKCGWQLVMTDANSSNSKQVSDIQNMIAQHVDLLVF 112 Query: 85 APVVETGWKPVLKEAKRAKIPVVIVDRNIKVDDDSL------FLTRIASDFSEEGRKIGQ 138 P E PV+ +AK+A IPV++VDR++ D S+ ++T I SDF ++G + Sbjct: 113 PPREEKPLAPVVLQAKKAGIPVILVDRDV---DQSVAKAGRDYITFIGSDFIDQGHRAAD 169 Query: 139 WLMDKTQGNCDIAELQGTVGATAAIDRAAGFNQVIANYPNAKIVRSQTGEFTRAKGKEVM 198 WL+ T G I EL+GT GA+AA DR GF+++IA P I+ SQ+G+F R KG++VM Sbjct: 170 WLVKATGGKAKIIELEGTTGASAANDRKKGFDEIIAKNPGMTIIASQSGDFARDKGRQVM 229 Query: 199 EGFLKAQNGQPLCAVWSHNDEMALGAVQAIKEAGLKPGKDILIVSVDGVPDYFKAMADGD 258 E L+A + AV++HNDEMALGA+ AIK AG +PGKDI IV++DG A+A G+ Sbjct: 230 ETLLQAH--PDVTAVYAHNDEMALGAIAAIKAAGKQPGKDIQIVTIDGTKGGMDAIAAGE 287 Query: 259 VNATVELSPYLGGPAFDAIDAYLKGNK 285 + A+V+ SP+ G A D Y KG K Sbjct: 288 LGASVQSSPFFGPLACDVAQRYAKGEK 314 Lambda K H 0.316 0.131 0.376 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: 270 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 313 Length of database: 339 Length adjustment: 28 Effective length of query: 285 Effective length of database: 311 Effective search space: 88635 Effective search space used: 88635 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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