Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate BPHYT_RS03795 BPHYT_RS03795 4-hydroxybenzoate transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__BFirm:BPHYT_RS03795 Length = 454 Score = 316 bits (809), Expect = 1e-90 Identities = 169/428 (39%), Positives = 260/428 (60%), Gaps = 6/428 (1%) Query: 12 LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71 ++V+ + + +Q +++LC L + +DG D AMG++AP++ EW + +A+LGPV S Sbjct: 13 IEVEQVLGETHHPAFQLLLLVLCGLCLVIDGFDAQAMGYVAPSVIGEWHVSKAALGPVFS 72 Query: 72 AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131 A+L GM+ GALG LADR GR+ VL+G+ F LA+ + T + L+ LRF+TGLGL Sbjct: 73 ASLFGMLLGALGLSVLADRIGRRPVLIGSTFFFALSMLATPFVTTIPALIALRFITGLGL 132 Query: 132 GAGMPNATTLLSEY-TP-ERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIG 189 G MPNA L+ E+ TP R+K +++ S CGF LG A GGFISA +IPAYGW ++ +G Sbjct: 133 GCIMPNAMALVGEFSTPAHRVKRMMLVS--CGFTLGAALGGFISAALIPAYGWRAVFWVG 190 Query: 190 GVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGSFSVPEQKAVAA 249 G +PLLLAL ++V LPES +FLV++ R +++ + L+ P + +A + V +K Sbjct: 191 GAVPLLLALAMLVALPESLQFLVLKGR-SERALRWLAKFNPALPIDANTRLVVREKGNGG 249 Query: 250 RSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQF 309 V A +F G T++LW FM L+ +Y L++WLPT+MRD+G S A +G + Q Sbjct: 250 APV-AELFRAGRGPVTLILWAISFMNLIDLYFLSNWLPTVMRDAGYSPSTAVIVGTVLQT 308 Query: 310 GGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGA 369 GGV+ + +GW ++R+ +V+ + + A + +G + L +V G CV G Sbjct: 309 GGVVGTLLLGWFIERFGFVRVLFVCFAGAALAVGTIGTVAHALPWLLLVVFAGGFCVVGG 368 Query: 370 QSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPA 429 Q A+ +LA FYPT R+TG+ W LGIGR G+++G G L+ L W+ + A +P Sbjct: 369 QPAVNALAGHFYPTTLRSTGIGWSLGIGRIGSVIGPLIGGQLIALNWSNAALFHAAALPV 428 Query: 430 ALATVGVI 437 + + VI Sbjct: 429 LCSALLVI 436 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: 566 Number of extensions: 31 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