Align proline porter II (characterized)
to candidate Ga0059261_2720 Ga0059261_2720 Arabinose efflux permease
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Korea:Ga0059261_2720 Length = 558 Score = 214 bits (546), Expect = 5e-60 Identities = 121/325 (37%), Positives = 177/325 (54%), Gaps = 16/325 (4%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 RK I A+SLG EW+DF +YG +A + FF G + + + AL F+ F +RP G Sbjct: 13 RKVIIASSLGTVFEWYDFYLYGLLATVISAKFFSGVNETTAFILALGAFAAGFAVRPFGA 72 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 L FG LGD GR+ +T+ +M +STF +G++PSY +IG+ API+L+ ++ QG ++GG Sbjct: 73 LVFGRLGDVVGRKYTFLVTMGLMGLSTFAVGILPSYASIGVAAPIILVALRLVQGLALGG 132 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 EY GA+ +VAE++P+ KRG SW+ + G VV+ I T +GEA F DWGWR+P Sbjct: 133 EYGGAATYVAEHAPEGKRGLFTSWIQTTATLGLFAALLVVIGIRTAIGEAAFADWGWRLP 192 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F +++ L + L++R L E+P FQ+ E+G K F E A WR+L T Sbjct: 193 FLVSILLLAVSLWIRLQLAESPVFQK---MKEEGTTS------KAPFTE-AFGQWRNLRT 242 Query: 264 ----CIGLVIATNVTYYMLLTYMPSYLSHNLHY-SEDHGVLIIIAIMIGMLFVQPVMGLL 318 +G V V +Y Y +L L +LI IA+ + F + G L Sbjct: 243 VLIVLLGAVAGQAVVWYTGQFYALFFLEKTLKVDGATANILIAIALALATPFF-VIFGAL 301 Query: 319 SDRFGRRPFVLLGSVALFVLAIPAF 343 SDR GR+ +L G + P F Sbjct: 302 SDRIGRKKIILTGCALAAISYFPTF 326 Score = 48.5 bits (114), Expect = 6e-10 Identities = 31/94 (32%), Positives = 55/94 (58%), Gaps = 2/94 (2%) Query: 353 LIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLV 411 LI A L L +++ G +A+ L +FPT IRY+A++ ++I + G PT+A +V Sbjct: 458 LIVALLFWLVLLVTAVYGPIAALLVEIFPTRIRYTAMSLPYHIGNGWFGGFLPTIAFAMV 517 Query: 412 ESSQNLMMPAYYLMVVAVVGLITGVT-MKETANR 444 ++ ++ +Y ++VAV+ LI G+ + ET R Sbjct: 518 AATGDIYYGLWYPIIVAVLTLILGLLFLPETFRR 551 Lambda K H 0.327 0.142 0.429 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: 745 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 558 Length adjustment: 35 Effective length of query: 465 Effective length of database: 523 Effective search space: 243195 Effective search space used: 243195 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 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