Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate 16092 b1981 shikimate transporter (NCBI)
Query= TCDB::M1Q159 (468 letters) >FitnessBrowser__Keio:16092 Length = 438 Score = 229 bits (584), Expect = 1e-64 Identities = 143/442 (32%), Positives = 235/442 (53%), Gaps = 37/442 (8%) Query: 15 KVIFASSAGTVIEWYDFYIFGALATTLASK-FYNTGTPIGDIIAWLGTFAVGFLVRPFGA 73 + S AG V++WYDF ++G A + ++ F+ +P +A TF VGFL RP G Sbjct: 22 RAALGSFAGAVVDWYDFLLYGITAALVFNREFFPQVSPAMGTLAAFATFGVGFLFRPLGG 81 Query: 74 IVFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGG 133 ++FG GD +GRK ++T+ +MG T LIG+LP+ +G WA I+L+T+R +QG A+GG Sbjct: 82 VIFGHFGDRLGRKRMLMLTVWMMGIATALIGILPSFSTIGWWAPILLVTLRAIQGFAVGG 141 Query: 134 QYGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLP 193 ++GGAA E AP+ K+ FY+S +Q GLL+S G++ + + + F WGWR+P Sbjct: 142 EWGGAALLSVESAPKNKKAFYSSGVQVGYGVGLLLSTGLVSLISMMTTDEQFLSWGWRIP 201 Query: 194 FMASILLVILSLWIRRALKESPLFQQLKDTKAVSKN--PLKESFANPYNLRWVLIALFGA 251 F+ SI+LV+ +LW+R ++ES F+Q + +A +K P+ E+ +IAL Sbjct: 202 FLFSIVLVLGALWVRNGMEESAEFEQQQHYQAAAKKRIPVIEALLRHPGAFLKIIAL--- 258 Query: 252 TMGQGVVWYTGQFYALFYLQKIFNTP---LIDSNLIVGAALLLSMPFFVFFGSLSDRIGR 308 + + + Y +AL Y + P ++ L+VG L++P F + L+DR GR Sbjct: 259 RLCELLTMYIVTAFALNYSTQNMGLPRELFLNIGLLVGGLSCLTIPCFAW---LADRFGR 315 Query: 309 KKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMV 368 ++V ++G L+ L+ +P + + A + +I + ++L + V+ V Sbjct: 316 RRVYITGTLIGTLSAFPFFMALEAQS---------IFWIVFFSIMLANIAHDMVVCVQQ- 365 Query: 369 YGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAI 428 E+F RY+ + Y + + V GG P I LI FAG W +AI Sbjct: 366 -----PMFTEMFGASYRYSGAGVGYQVASVVGGGFTPFIAAALITY----FAGNWHSVAI 416 Query: 429 ---AGICLVVGF--LLIKETNK 445 AG CL+ LL+K++ + Sbjct: 417 YLLAG-CLISAMTALLMKDSQR 437 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: 613 Number of extensions: 37 Number of successful extensions: 5 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: 438 Length adjustment: 33 Effective length of query: 435 Effective length of database: 405 Effective search space: 176175 Effective search space used: 176175 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