Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate RR42_RS35155 RR42_RS35155 MFS transporter
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Cup4G11:RR42_RS35155 Length = 459 Score = 255 bits (652), Expect = 2e-72 Identities = 144/428 (33%), Positives = 231/428 (53%), Gaps = 5/428 (1%) Query: 12 LDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPVMS 71 +D+ ++ +R+ +++L C LI+ DG D A +G P++ + G+D S G ++S Sbjct: 4 IDIHKLADEARFNRFHAQILLWCALIIIFDGYDLAVVGIALPSIMKGMGVDATSAGFMVS 63 Query: 72 AALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGLGL 131 AAL GM+FGA+ G +ADR GR+ + +L+F F+ A+ + ++ V RFL GLG+ Sbjct: 64 AALFGMMFGAIFMGTVADRIGRRRAIAICILLFSVFTAAAGFTSDPVTFSVTRFLAGLGI 123 Query: 132 GAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIGGV 191 G MPN ++EY+P +++ +VT MF G+++G + MI +YGW S+ + Sbjct: 124 GGVMPNVVAQMTEYSPRKIRGTMVTLMFSGYSVGGMLAALLGKGMIESYGWQSVF-LAAS 182 Query: 192 LPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPIAPQVVAEAGS-FSVPEQKAVAAR 250 LP LL V++ +PES FL +R+ D ++ S + P + G F++P A Sbjct: 183 LPALLIPVILKSMPESMPFL-IRSGQIDALKHVASRLEPGYQPQPGDRFALPAGDK-AGD 240 Query: 251 SVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALFQFG 310 + +F G T++ W+ +FM L +VY L+SWL +M +G S+ A + FG Sbjct: 241 APIGKLFQDGRGFSTVMFWVAFFMCLFMVYALSSWLAKMMAGAGYSLGSALTFVLVLNFG 300 Query: 311 GVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVNGAQ 370 +L A+G GW DR+N V+ Y LA V +G + +L LV +AG G Q Sbjct: 301 AMLGAIGGGWLADRFNIKYVLVGMYALAAVSITLLGYPVPT-ALLFVLVALAGASTIGTQ 359 Query: 371 SAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLVPAA 430 + A +FYP RATG+ W GIGR GAIL L+G+ +Q A+ +PA Sbjct: 360 IVTYAYAGQFYPMAVRATGIGWASGIGRSGAILAPIVIGALVGMSLPLQQNFVAIAIPAV 419 Query: 431 LATVGVIV 438 +A + V++ Sbjct: 420 IAMIAVLL 427 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: 572 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 448 Length of database: 459 Length adjustment: 33 Effective length of query: 415 Effective length of database: 426 Effective search space: 176790 Effective search space used: 176790 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