Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate AZOBR_RS26920 AZOBR_RS26920 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__azobra:AZOBR_RS26920 Length = 454 Score = 451 bits (1159), Expect = e-131 Identities = 224/437 (51%), Positives = 303/437 (69%), Gaps = 1/437 (0%) Query: 10 KSLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPV 69 +S+DVQ+F+N+ P SRYQW V LCF IV LDG DTAA+G+IAP+L+ EWGI R +L PV Sbjct: 5 RSVDVQAFLNEHPFSRYQWLVFALCFFIVLLDGFDTAAIGYIAPSLTTEWGIARPALAPV 64 Query: 70 MSAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGL 129 +SAAL G+ FGAL +GPLADRFGRK +L+G+VLV G LASA++ N+DQL++LRF+TGL Sbjct: 65 LSAALFGLAFGALSAGPLADRFGRKAILIGSVLVIGTACLASAFSGNLDQLVMLRFVTGL 124 Query: 130 GLGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIG 189 GLGA MPNA TL+SEY PE ++++ +MFCGF LG A GGF++A MIP +GW S+LV+G Sbjct: 125 GLGAAMPNAVTLMSEYCPEGRRAMVTNAMFCGFPLGAAFGGFLAAWMIPLWGWRSVLVLG 184 Query: 190 GVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA 249 G+ PL+LA VL+V LPES R++V N ++IR L I+ AG + A A Sbjct: 185 GIAPLVLAAVLLVLLPESVRYMVAHNHPVERIRAVLRRISETAAGAAGFVMTEKAPATKA 244 Query: 250 RSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQF 309 R+ AV+ S Y +G+++LW+ YFMGLVI Y L +W+P L +D+G + AA I ALF Sbjct: 245 RNGIAVVLSRGYLVGSVMLWVAYFMGLVIFYALINWMPILFKDAGLAPRDAALIAALFPL 304 Query: 310 GGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGA 369 GGV AV GW MDR+N +++I ++L YA+GQ GN+ +L V AG +N A Sbjct: 305 GGV-GAVLSGWLMDRFNANRIIAFGFVLTYGAVYAIGQVAGNVGLLVVTVFAAGTIMNTA 363 Query: 370 QSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPA 429 Q+++P+LAA FYPT GRATGV+WMLG+GRFG I G++ A L +F + + VP Sbjct: 364 QTSLPALAASFYPTHGRATGVAWMLGLGRFGGIGGSFLVAELARRQLDFTSIFAIVAVPG 423 Query: 430 ALATVGVIVKGLVSHAD 446 +A + ++VK V D Sbjct: 424 LVAALALLVKQFVHPED 440 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: 619 Number of extensions: 30 Number of successful extensions: 2 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 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