Align 4-hydroxybenzoate transporter PcaK (characterized)
to candidate RR42_RS31660 RR42_RS31660 hypothetical protein
Query= SwissProt::Q51955 (448 letters) >FitnessBrowser__Cup4G11:RR42_RS31660 Length = 458 Score = 349 bits (895), Expect = e-100 Identities = 175/434 (40%), Positives = 270/434 (62%), Gaps = 4/434 (0%) Query: 10 KSLDVQSFINQQPLSRYQWRVVLLCFLIVFLDGLDTAAMGFIAPALSQEWGIDRASLGPV 69 K ++V SFI+++P+ RYQ +++L FL+V DG+D A MGF AP + + WGI ++ +G + Sbjct: 5 KKINVVSFIDERPVGRYQIFIIILVFLVVAFDGMDVAIMGFAAPEIIRTWGITKSQMGSI 64 Query: 70 MSAALIGMVFGALGSGPLADRFGRKGVLVGAVLVFGGFSLASAYATNVDQLLVLRFLTGL 129 + A G+ GAL +GP+ DR+GRK +L +V FG +L S+ A +V+ L+ LR LTGL Sbjct: 65 LGAVFFGVAVGALIAGPIGDRYGRKLILTASVFWFGVLTLVSSQAPDVNTLITLRILTGL 124 Query: 130 GLGAGMPNATTLLSEYTPERLKSLLVTSMFCGFNLGMAGGGFISAKMIPAYGWHSLLVIG 189 GLGA +PNA TL+SEY P R +SL+VT ++ GF G A G I+A ++ +GW ++ IG Sbjct: 125 GLGAALPNAVTLISEYVPVRKRSLIVTIVYSGFTGGAAVAGLIAAWLLQVFGWRVMIAIG 184 Query: 190 GVLPLLLALVLMVWLPESARFLVVRNRGTDKIRKTLSPI--APQVVAEAGSFSVPEQKAV 247 G+LP++LAL+L +WLPES FL ++ + I K L I V+++A +F +P Sbjct: 185 GLLPIVLALILAIWLPESVAFLTLKGKRLAAIPKILRKIDRGSSVLSDA-TFWIPTPVDQ 243 Query: 248 AARSVFAVIFSGTYGLGTMLLWLTYFMGLVIVYLLTSWLPTLMRDSGASMEQAAFIGALF 307 + SV A++F+ Y +GT LL + YFMG+ Y++ +WLP + +D+G ++ Q I L Sbjct: 244 SKGSV-AILFTKAYAMGTFLLCVAYFMGVCATYVMVNWLPVIAKDAGFTLGQGVVITTLI 302 Query: 308 QFGGVLSAVGVGWAMDRYNPHKVIGIFYLLAGVFAYAVGQSLGNITVLATLVLIAGMCVN 367 GG + ++ +G MDR PH V+ +L+AG F ++ + N L L+ G + Sbjct: 303 TLGGPIGSICIGAIMDRVRPHWVLVPTFLIAGAFLASLSVAPRNFGALCVLMFALGCFFH 362 Query: 368 GAQSAMPSLAARFYPTQGRATGVSWMLGIGRFGAILGAWSGATLLGLGWNFEQVLTALLV 427 G+ + + +L+A +PT R+TG+SWM G GR GAI + GAT++G GW Q+ AL V Sbjct: 363 GSMTGLQALSAMSFPTAARSTGISWMHGFGRLGAIASGFIGATMMGWGWGLGQIFLALAV 422 Query: 428 PAALATVGVIVKGL 441 P +A V V G+ Sbjct: 423 PMVVAACAVAVLGM 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: 592 Number of extensions: 41 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: 458 Length adjustment: 33 Effective length of query: 415 Effective length of database: 425 Effective search space: 176375 Effective search space used: 176375 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