Align fusion of gluconokinase and the small permease component of the D-gluconate TRAP transporter (characterized)
to candidate WP_090448378.1 BLS63_RS24290 gluconokinase
Query= reanno::psRCH2:GFF2080 (376 letters) >NCBI__GCF_900100495.1:WP_090448378.1 Length = 361 Score = 469 bits (1207), Expect = e-137 Identities = 246/361 (68%), Positives = 276/361 (76%), Gaps = 2/361 (0%) Query: 18 MGVSGSGKTETSHAVADALGLPHIEADNFHPAENVARMRAGTPLSDADRMEWLHALIAEM 77 MGVSGSGK++ S AVA LG HIEAD FHP ENV RMRAG PLSD DR WL ALI EM Sbjct: 1 MGVSGSGKSDISQAVARQLGWRHIEADQFHPRENVERMRAGIPLSDDDRSHWLDALIREM 60 Query: 78 QRTLAAGSGFVLACSALKRSYRELLRSAVPELRFAHLAIDYETAVQRVGGRAGHFMPISL 137 Q A+G GFVLACSALKRSYRE LR+AVP LRFAHL ID TA+QRVG R GHFMP SL Sbjct: 61 QAAEASGEGFVLACSALKRSYRERLRAAVPGLRFAHLDIDQATALQRVGARPGHFMPTSL 120 Query: 138 VDSQFATLESPEGEPGVLTVDASQPREGVLRQIVEWMQGSGLDELIETRVDLSSRPFDSA 197 VDSQFATLE P GE GVL+VDA+Q R V+ Q+ W+ G L+ IE VD S++ FDSA Sbjct: 121 VDSQFATLEDPSGEYGVLSVDAAQSRAVVVAQVCAWVHGKSLEVEIEEAVDFSAQTFDSA 180 Query: 198 TT--APPLTNEPIYSGRVAQHFDRLTDWLMAALMAFMVIVVFSSVVLRYAFGTGWTGAEE 255 LT EPIY+G +A+ FDRLTD LMA LM FMV+VVF +VVLRYAF +GW GAEE Sbjct: 181 NKEGGAHLTGEPIYTGALARLFDRLTDGLMAVLMGFMVLVVFGNVVLRYAFDSGWAGAEE 240 Query: 256 LSRLAFVWLVFVGVASSMRRGELMSFSMLRDRFPRLFRRVVDSLSWLLVAAASCLAAWGG 315 LSRLAFVWLVF+GVASSMRRGELMSFS++RDRFP+ RR++DS SWLLVAAAS LA WG Sbjct: 241 LSRLAFVWLVFIGVASSMRRGELMSFSLVRDRFPQAVRRLIDSASWLLVAAASGLATWGA 300 Query: 316 WNQMQFGWTINSPVVGYPLGLAMLPVAASMVALAVLALLQLVNVWRRDQPSATAAANVTA 375 W QMQFGW S VVGY L LAMLPV A M L +LAL+QL+NVWRR A++ ANVT Sbjct: 301 WQQMQFGWGNISAVVGYSLALAMLPVLACMAVLVLLALVQLLNVWRRPYGLASSLANVTV 360 Query: 376 D 376 D Sbjct: 361 D 361 Lambda K H 0.322 0.133 0.401 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: 423 Number of extensions: 8 Number of successful extensions: 2 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: 376 Length of database: 361 Length adjustment: 30 Effective length of query: 346 Effective length of database: 331 Effective search space: 114526 Effective search space used: 114526 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 (22.0 bits) S2: 49 (23.5 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