Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate WP_011382707.1 AMB_RS01320 MFS transporter
Query= SwissProt::Q51955 (448 letters) >NCBI__GCF_000009985.1:WP_011382707.1 Length = 465 Score = 427 bits (1099), Expect = e-124 Identities = 217/431 (50%), Positives = 301/431 (69%), Gaps = 5/431 (1%) Query: 12 LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71 L++Q+F+N+ S YQW V LCF +V LDG DTAA+G+IAP+L +EWGI + +LGPV+S Sbjct: 7 LNIQTFLNESRFSPYQWTVFALCFFVVLLDGFDTAAIGYIAPSLLKEWGIAKPALGPVLS 66 Query: 72 AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131 AAL G+ GAL +GPLADRFGR+ VL G+ L+F SLAS++A ++D L VLRF+TG+GL Sbjct: 67 AALFGLAAGALSAGPLADRFGRRLVLTGSTLLFALASLASSFAGSLDGLTVLRFVTGIGL 126 Query: 132 GAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGV 191 GA MPNA TL+SEY P++ +SLL +MF GF LG A GGF++A +IP +GW S+LV+GG+ Sbjct: 127 GAAMPNAVTLISEYCPDQRRSLLTNAMFAGFPLGAALGGFLAAWIIPQWGWRSVLVLGGI 186 Query: 192 LPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA-- 249 PL L ++ V LPES R++V R + ++IRK LS I+ A+A F + E A A Sbjct: 187 APLALVALMAVSLPESIRYMVARRQPAERIRKVLSRISAS-AAQAQGFVMTEAAAKVAPT 245 Query: 250 -RSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQ 308 ++ V+ S +Y +G++++WL YFMGLVI Y L +W+P L++D+G + A I ALF Sbjct: 246 GKAGLGVVLSKSYLVGSVMMWLAYFMGLVIFYGLINWMPLLLKDAGLDPKSATLISALFP 305 Query: 309 FGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNG 368 GGV A+ GW MDR N +KVI Y+L + +A+GQ++GN+ VL LVL+AG +N Sbjct: 306 LGGV-GAIFFGWLMDRANGNKVIAAGYVLTALLIFAIGQAVGNVGVLVLLVLVAGTLMNT 364 Query: 369 AQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVP 428 AQS+MP+LAA FYPT GRATGV+WMLG+GRFG I G+ A L F ++ T + +P Sbjct: 365 AQSSMPALAAGFYPTSGRATGVAWMLGMGRFGGIAGSTLVAELSRRQLGFSEMFTIIAIP 424 Query: 429 AALATVGVIVK 439 +A ++VK Sbjct: 425 GLIAAAALLVK 435 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: 620 Number of extensions: 25 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: 465 Length adjustment: 33 Effective length of query: 415 Effective length of database: 432 Effective search space: 179280 Effective search space used: 179280 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