Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate H281DRAFT_03848 H281DRAFT_03848 MFS transporter, AAHS family, 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Burk376:H281DRAFT_03848 Length = 406 Score = 396 bits (1017), Expect = e-115 Identities = 206/403 (51%), Positives = 281/403 (69%), Gaps = 3/403 (0%) Query: 10 KSLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPV 69 + +DVQ IN+ P S +Q + +CFLIV +DG DTAA+GFIAP+L QEW I +A+L PV Sbjct: 5 RPVDVQVLINEHPFSPFQRLIFAMCFLIVLMDGFDTAAIGFIAPSLLQEWHIGKAALAPV 64 Query: 70 MSAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGL 129 +SAAL G+ GAL SGPL+DR GR+ VL AVL+FG SA+A ++ QL LRF+TG+ Sbjct: 65 LSAALFGLACGALLSGPLSDRLGRRVVLTSAVLLFGVSCFGSAFAFDLTQLTTLRFITGV 124 Query: 130 GLGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIG 189 GLGA MPNA TL+SE+ P++ ++ +V MFCGF LG A GGF++A MIP +GW S+L+ G Sbjct: 125 GLGAAMPNAVTLMSEFCPDKRRATIVNLMFCGFPLGAALGGFLAAWMIPHFGWRSVLLFG 184 Query: 190 GVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA 249 G +PLLL ++LM+ LPES R+LV + + KIRK L I+ A A SF + E AA Sbjct: 185 GAVPLLLWMLLMLKLPESIRYLVAKRQPAIKIRKVLVQISASANA-AESFIMRETVEHAA 243 Query: 250 RSV-FAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQ 308 S + S ++ +G+++LWL YFMGLVI Y L +W+P L++++G S ++AA + ALF Sbjct: 244 GSGGIRIALSRSFLVGSLMLWLCYFMGLVIFYGLVNWMPVLLKEAGLSPQRAALVSALFP 303 Query: 309 FGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNG 368 GGV V G MDR+NP++V+ Y L V YA+GQ++GN+ +L V +AG VN Sbjct: 304 LGGV-GTVLCGMLMDRFNPNRVVAAAYALGAVSVYAIGQAVGNLGLLMCAVFVAGALVNT 362 Query: 369 AQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATL 411 AQ++MP+LAA FYPT GR TGV+WMLG+GRFG I G++ A L Sbjct: 363 AQASMPALAAAFYPTAGRGTGVAWMLGVGRFGGIAGSFLVAEL 405 Score = 38.9 bits (89), Expect = 3e-07 Identities = 52/191 (27%), Positives = 79/191 (41%), Gaps = 20/191 (10%) Query: 227 PIAPQVVAEAGSFSVPEQKAVAARSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWL 286 P+ QV+ FS P Q+ + A V+ G + T +G + LL W Sbjct: 6 PVDVQVLINEHPFS-PFQRLIFAMCFLIVLMDG---------FDTAAIGFIAPSLLQEW- 54 Query: 287 PTLMRDSGASMEQAAFIGALFQFGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVG 346 + + + A + AA G G +LS G DR V+ LL GV + Sbjct: 55 -HIGKAALAPVLSAALFG--LACGALLS----GPLSDRLGRRVVLTSAVLLFGVSCFGSA 107 Query: 347 QSLGNITVLATLVLIAGMCVNGAQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAW 406 + ++T L TL I G+ + A +L + F P + RAT V+ M GA LG + Sbjct: 108 FAF-DLTQLTTLRFITGVGLGAAMPNAVTLMSEFCPDKRRATIVNLMFCGFPLGAALGGF 166 Query: 407 SGATLL-GLGW 416 A ++ GW Sbjct: 167 LAAWMIPHFGW 177 Lambda K H 0.325 0.140 0.424 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: 568 Number of extensions: 31 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 448 Length of database: 406 Length adjustment: 32 Effective length of query: 416 Effective length of database: 374 Effective search space: 155584 Effective search space used: 155584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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