Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate BWI76_RS02250 BWI76_RS02250 proline/betaine transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Koxy:BWI76_RS02250 Length = 500 Score = 238 bits (607), Expect = 3e-67 Identities = 154/458 (33%), Positives = 243/458 (53%), Gaps = 34/458 (7%) Query: 15 KVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAI 74 K I A+S G +EW+DF ++G +A L F+ P +IA LGTF+V FL+RP G + Sbjct: 25 KAITAASLGNAMEWFDFGVYGFVAYALGKVFFPDANPSVQMIAALGTFSVPFLIRPLGGL 84 Query: 75 VFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQ 134 FG +GD GR+ ITI IM TF IGL+P+ +G WA I+L+ ++ QG ++GG+ Sbjct: 85 FFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYATIGIWAPILLLLCKMAQGFSVGGE 144 Query: 135 YGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPF 194 Y GA+ FVAE++P KRGF SW+ + G ++ GV+++ +GE +F WGWR+PF Sbjct: 145 YTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVMGAGVVVLISSVVGEENFLSWGWRIPF 204 Query: 195 MASILLVILSLWIRRALKESPLFQQ------LKDTKAVSKNPLKESFANPYNLRW-VLIA 247 ++ L I+ L++R AL+E+P FQQ D + + + P K SF W L+ Sbjct: 205 FLALPLGIIGLYLRHALEETPAFQQHVDKMEQGDREGLQEGP-KVSFKEIATKHWRSLLT 263 Query: 248 LFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFF-VFFGSLSDRI 306 G + V +Y Y YL + D +++ A+++ M F G LSDR Sbjct: 264 CIGLVISTNVTYYMLLTYMPSYLSHNLHYS-EDHGVLIIIAIMVGMLFVQPVIGMLSDRF 322 Query: 307 GRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLL---VFIQVI 363 GR+ +L G +A FA + P A+I N +LGL+ + + + Sbjct: 323 GRRPFIL-------------IGSVALFALSIP------AFIMINSNVLGLIFAGLLVLAV 363 Query: 364 YVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLW 423 + G +A+ L +FPT IR+++++ ++I + + GL P + L+ +T N + Sbjct: 364 VLNCFIGVMASSLPAMFPTHIRFSALASAFNI-SVLIAGLTPTLAAWLVESTQNLMMPAY 422 Query: 424 WPMAIAGICLVVGFLLIKETNKVDISDASTSISVKHEA 461 + M IA I L+ G L +KET + A+ + S EA Sbjct: 423 YLMVIAVIGLITG-LSMKETANRPLKGATPAASDIQEA 459 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: 712 Number of extensions: 51 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: 468 Length of database: 500 Length adjustment: 34 Effective length of query: 434 Effective length of database: 466 Effective search space: 202244 Effective search space used: 202244 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: 52 (24.6 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