Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate BPHYT_RS07110 BPHYT_RS07110 LysR family transcriptional regulator
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__BFirm:BPHYT_RS07110 Length = 437 Score = 252 bits (643), Expect = 2e-71 Identities = 147/425 (34%), Positives = 235/425 (55%), Gaps = 36/425 (8%) Query: 19 ASSAGTVIEWYDFYIFGALATTLASKFYNTGT-PIGDIIAWLGTFAVGFLVRPFGAIVFG 77 A+ GT IEWYDFYI+ + + K + G+ P +A GTFAVGF RPFG +VFG Sbjct: 20 AAFVGTTIEWYDFYIYATASALIFGKLFFPGSDPFFATLASFGTFAVGFFARPFGGLVFG 79 Query: 78 RIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYGG 137 +GD +GRK + T+ IMG T IG LPT G WA ++L+ +R+ QG+A+GG++GG Sbjct: 80 HLGDRIGRKKALVATLAIMGVGTVGIGFLPTYASAGVWAPVLLVLLRVAQGIAIGGEWGG 139 Query: 138 AATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPFMAS 197 A +EHAPQG+R F+ S+ Q + GL++SL + S+ + F WGWRLPF+AS Sbjct: 140 AVLMASEHAPQGRRTFFASFAQLGSPAGLILSL-LAFRAVASMDKDAFLGWGWRLPFLAS 198 Query: 198 ILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMGQGV 257 +L+++ L IR + ESP F+ LK + V+ P+ E + + R +L+ L +G Sbjct: 199 AVLLVVGLLIRAGVDESPEFKALKAQRRVAALPVAEVVRDAW--RTLLLCLGANVIGVAG 256 Query: 258 VWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLS-MPFFVFFGS--LSDRIGRKKVMLS 314 W+ F + Q T +D +LI+ +++ + F GS + RIG + + Sbjct: 257 AWFVNTFMLNYTTQ----TLGLDRSLILDCLFVVAFIQLFTQLGSGWFAQRIGTGRFLKG 312 Query: 315 GMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYGPIAA 374 LA+L+ YP++ L++ P +++G + + V+ ++ Y +A Sbjct: 313 AAALAMLSPYPMFALVSTGRPV--------------AIVIG--IALAVMCMSSSYAVMAG 356 Query: 375 FLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAI-----A 429 F+ FP ++RY+++SL Y + + GGL P+IG +L + + G WWP+A+ A Sbjct: 357 FMSTAFPVRVRYSAISLSYQVCAALAGGLTPLIGTLL----AHRYPGAWWPLAVFYSVLA 412 Query: 430 GICLV 434 G+ LV Sbjct: 413 GVSLV 417 Lambda K H 0.328 0.144 0.450 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: 639 Number of extensions: 38 Number of successful extensions: 8 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: 468 Length of database: 437 Length adjustment: 33 Effective length of query: 435 Effective length of database: 404 Effective search space: 175740 Effective search space used: 175740 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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