Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate Pf1N1B4_5977 Transporter, MFS superfamily
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5977 Length = 465 Score = 257 bits (657), Expect = 5e-73 Identities = 152/460 (33%), Positives = 253/460 (55%), Gaps = 21/460 (4%) Query: 2 MQTSSPPTPKGIWKVIFASSAGTVIEWYDFYIFGALATTLASK--FYNTGTPIGDIIAWL 59 + T S TP G+ +V+ A+ AGTV EWY+F+++G + + + F T +PI IIA Sbjct: 5 LHTQSATTPSGLKRVVAAAMAGTVAEWYEFFLYGTASALVFGQLFFRQTDSPIDGIIAAF 64 Query: 60 GTFAVGFLVRPFGAIVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGII 119 +AVGFL RP G +VFG GD GRK +++ ++G TFL+G LP D +G A ++ Sbjct: 65 ALYAVGFLARPLGGLVFGHYGDKFGRKRLLQLSLVVVGITTFLMGCLPGFDQIGYAAPVL 124 Query: 120 LITMRILQGLALGGQYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRIS 179 L+ +R++QG A GG++GGA V+EH P +RGF+ SW Q G L++ +L+ + Sbjct: 125 LVLLRLIQGFAFGGEWGGAILLVSEHCPDNRRGFWASWPQAGVPAGNLVATVALLLLSSN 184 Query: 180 LGEADFNEWGWRLPFMASILLVILSLWIRRALKESPLFQQLKDTKA-VSKNPLKESFANP 238 L E F WGWR+ F S ++V++ WIR ++ ++P+F++ + +A + + L Sbjct: 185 LSEEQFLAWGWRVAFWFSAVVVLIGYWIRTSVDDAPIFKEAQARQAQIKQQQLGVVEVLR 244 Query: 239 YNLRWVLIALFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVF 298 ++ R VL+ + GA + +++YT +++ YL+ + + + L++ A L+ Sbjct: 245 HHWRAVLVGI-GARFAENILYYTVVTFSITYLKLVVHKDTSEILLLMFGAHLVHFFLIPL 303 Query: 299 FGSLSDRIGRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLV 358 G LSD +GRK V L+G AVLT + +G + F D G ++L +ILGL + Sbjct: 304 MGYLSDIVGRKPVYLTG---AVLTAF--WGFV-GFPMMDTGNNWLI----MAAIILGLGI 353 Query: 359 FIQVIYVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGND 418 +M Y P +A + E+FPT +RYT++SL Y + G L P+I + L+N + Sbjct: 354 ------ESMTYAPYSALMAEMFPTHVRYTALSLCYQVAPIFAGSLAPLIAITLLNKYHSS 407 Query: 419 FAGLWWPMAIAGICLV-VGFLLIKETNKVDISDASTSISV 457 W+ + A I +V VG + + DA ++ + Sbjct: 408 TPIAWYLVGAALISIVAVGLTRETRGKSLHLVDAESAARI 447 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: 34 Number of successful extensions: 7 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: 465 Length adjustment: 33 Effective length of query: 435 Effective length of database: 432 Effective search space: 187920 Effective search space used: 187920 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