Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate GFF2891 PS417_14785 glycine/betaine ABC transporter
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__WCS417:GFF2891 Length = 500 Score = 241 bits (614), Expect = 5e-68 Identities = 150/455 (32%), Positives = 243/455 (53%), Gaps = 28/455 (6%) Query: 15 KVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAI 74 K I A++ G +EW+DF ++G +A L F+ +P +IA LGTF+V FL+RP G + Sbjct: 26 KAITAAALGNAMEWFDFGVYGFVAYVLGKVFFPDASPSVQMIAALGTFSVPFLIRPLGGL 85 Query: 75 VFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQ 134 FG +GD GR+ TI IM TF IGL+P+ +G WA I+L+ ++ QG ++GG+ Sbjct: 86 FFGALGDKYGRQKVLAATIVIMSLSTFAIGLIPSYASIGIWAPILLLLCKMAQGFSVGGE 145 Query: 135 YGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPF 194 Y GA+ FVAE+AP KRGF SW+ + G ++ GV+++ LGEADF WGWRLPF Sbjct: 146 YTGASIFVAEYAPDRKRGFLGSWLDFGSIAGFVLGAGVVVLISSILGEADFESWGWRLPF 205 Query: 195 MASILLVILSLWIRRALKESPLFQQ------LKDTKAVSKNPLKESFANPYNLRW-VLIA 247 ++ L I+ L++R AL+E+P FQQ D + ++ P K SF W L+ Sbjct: 206 FLALPLGIIGLYLRHALEETPAFQQHMDKMEQGDREGLTHGP-KVSFKEVATKHWRSLLT 264 Query: 248 LFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFF-VFFGSLSDRI 306 G V +Y Y YL + +S +++ A+++ M F F G +SD+I Sbjct: 265 CIGIVAATNVTYYMLLTYMPSYLSHNLHYK-ENSGVLIIIAIMVGMLFVQPFIGFISDKI 323 Query: 307 GRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVT 366 GRK +++G + + P + L+ + IG + GLL+ + + Sbjct: 324 GRKPFIIAGSIGLLFLSIPAFMLITS------------GKIGL--IFAGLLIL--AVILN 367 Query: 367 MVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPM 426 G +A+ L +FPT +RY++++ +++ + + GL P L+ +T + + ++ M Sbjct: 368 FFIGVMASTLPAMFPTHLRYSALASAFNV-SVLIAGLTPTAVAWLVESTNDLYMPAYYLM 426 Query: 427 AIAGICLVVGFLLIKETNKVDISDASTSISVKHEA 461 A + L+ G L +KET + A+ + S EA Sbjct: 427 VFAVVGLITG-LTMKETANKPLRGAAPAASDMEEA 460 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: 720 Number of extensions: 50 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