Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate PfGW456L13_2328 L-Proline/Glycine betaine transporter ProP
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2328 Length = 459 Score = 258 bits (660), Expect = 2e-73 Identities = 157/440 (35%), Positives = 235/440 (53%), Gaps = 27/440 (6%) Query: 15 KVIFASSAGTVIEWYDFYIFGALATTLASK-FYNTGTPIGDIIAWLGTFAVGFLVRPFGA 73 KV AS GT +EWYD ++F + + +K F+ P+ + GTFA +L R GA Sbjct: 22 KVAVASVIGTTVEWYDLFVFATASALVFNKVFFPDFVPLIGTLLAFGTFASAYLARIVGA 81 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 +FG GD +GRK LI++ MG+ TF IGLLP +G WA I+L+ +R++QGLALGG Sbjct: 82 ALFGHFGDRLGRKSMLLISLLTMGAATFAIGLLPDFATIGIWAPILLLLLRVVQGLALGG 141 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGA EHAP KRG Y SW+Q G +I+ L+ L D WGWR+P Sbjct: 142 EWGGAVLMAVEHAPANKRGLYGSWVQIGVPAGTMIANLAFLLIAAWLSPEDLLAWGWRIP 201 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFG-AT 252 F+AS+LL+ + L+IR + E+P F ++K+ + K PL E F W + L G AT Sbjct: 202 FLASVLLIAVGLYIRLNISETPAFNKVKEAEVQVKMPLAEVFRK----YWKQVLLGGIAT 257 Query: 253 MGQGVVWYTGQFYALFY-LQKI-FNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKK 310 M G + + L Y Q + F+ ++ +++ A + M FG+LSDR GRK Sbjct: 258 MSTGASFNIIVAFGLTYGTQNLGFSRSVMLGVVLLSCAWCIVM--LPVFGALSDRFGRKP 315 Query: 311 VMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYG 370 +++ G++ L +P++ LM + V+ G L+ + YG Sbjct: 316 IIVGGIIAEALVAFPMFWLMDTKE--------------LSMVVFGYLLLMTAFAAN--YG 359 Query: 371 PIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAG 430 PIA FL ELF T++RY+ +S+ Y + + P++ L+ ATG + W+ + A Sbjct: 360 PIATFLAELFGTRVRYSGLSISYMLSGLLGSAATPIVTTALLAATGKGSSVAWYMIGAAL 419 Query: 431 ICLVVGFLLIKETNKVDISD 450 I L V LL+ ET K DIS+ Sbjct: 420 ISL-VALLLLTETFKKDISE 438 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: 703 Number of extensions: 33 Number of successful extensions: 6 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: 459 Length adjustment: 33 Effective length of query: 435 Effective length of database: 426 Effective search space: 185310 Effective search space used: 185310 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