Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate WP_011766270.1 AZO_RS12820 MFS transporter
Query= SwissProt::Q51955 (448 letters) >NCBI__GCF_000061505.1:WP_011766270.1 Length = 454 Score = 447 bits (1150), Expect = e-130 Identities = 224/431 (51%), Positives = 302/431 (70%), Gaps = 3/431 (0%) Query: 10 KSLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPV 69 + +DVQ+FINQ P SR+QW V LCF+IV LDG DTAA+G+IAP+L EWG+ R +L PV Sbjct: 5 RPVDVQAFINQHPFSRFQWSVFALCFVIVLLDGFDTAAIGYIAPSLINEWGVSRPALAPV 64 Query: 70 MSAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGL 129 +SAAL G+ GAL +GPLADRFGRK VLVG+VL+FG LASA+ ++ L +RF+TGL Sbjct: 65 LSAALFGLAGGALSAGPLADRFGRKEVLVGSVLLFGVACLASAFVADLTMLTAMRFVTGL 124 Query: 130 GLGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIG 189 GLGA MPNA TL+SEY P++ +++L +MFCGF LG A GGF+++ MIP +GW S+L++G Sbjct: 125 GLGAAMPNAVTLMSEYCPDQRRAMLTNAMFCGFPLGAAFGGFLASWMIPHFGWRSVLMLG 184 Query: 190 GVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVA- 248 G+ PL+L L+L++ LPES R++V R ++IR LS I+ A+AGSF + E + A Sbjct: 185 GIAPLVLVLLLVLVLPESVRYMVARAYPAERIRAVLSRIS-ATAAQAGSFVMSETRPAAN 243 Query: 249 ARSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQ 308 R V+FS Y +G+++LWL YFMGLVI Y L +W+P L +D+G + A I ALF Sbjct: 244 GRRGLGVVFSREYRVGSLMLWLAYFMGLVIFYALINWMPILFKDAGLEPQHATLISALFP 303 Query: 309 FGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNG 368 GGV AV GW MDR+N + +I + Y V YA+GQ GN+ L LV +AG +N Sbjct: 304 LGGV-GAVFFGWLMDRFNGNFIIAVGYAFTAVSIYAIGQVAGNVGALVVLVFVAGTIMNT 362 Query: 369 AQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVP 428 AQS+MP+LAA FYPT GRATGV+WMLGIGRFG I G++ A L F+Q+ + +P Sbjct: 363 AQSSMPALAAGFYPTAGRATGVAWMLGIGRFGGIAGSFLVAELSRRQLAFDQIFMVVALP 422 Query: 429 AALATVGVIVK 439 A+A + ++VK Sbjct: 423 GAIAAIALLVK 433 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: 615 Number of extensions: 31 Number of successful extensions: 3 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: 448 Length of database: 454 Length adjustment: 33 Effective length of query: 415 Effective length of database: 421 Effective search space: 174715 Effective search space used: 174715 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 24 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