Align proline porter II (characterized)
to candidate Pf6N2E2_1930 L-Proline/Glycine betaine transporter ProP
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1930 Length = 456 Score = 236 bits (602), Expect = 1e-66 Identities = 138/420 (32%), Positives = 235/420 (55%), Gaps = 8/420 (1%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 R+++ A ++GN E +DF V+GF L FFPG+D + +++ A ++V F+ RPLGG Sbjct: 10 RRSLAAGAIGNFGEIYDFAVFGFSIPILSVHFFPGSDRTAALLSTFAVYAVAFVARPLGG 69 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 L FG L D+ GR +++A+T+ +M++ T IGL+P+Y TIGI AP+LLL+C++AQG ++GG Sbjct: 70 LMFGYLADRLGRIRVMAMTVWLMALGTAIIGLLPTYATIGIAAPLLLLLCRIAQGLALGG 129 Query: 144 EYTGASIFVAEYSPDRKRGF-MGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRI 202 E TG++ ++ E +P+ +RG+ +G L F + V+ AG+VV + G+ + DW WRI Sbjct: 130 ETTGSTSYIVESAPENRRGYWLGFTLIFSHLPNAVV-AGLVVALQLGAGDQAYSDWAWRI 188 Query: 203 PFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLL 262 PF + +G++G +LR ++E ++Q + ++ P ++ I R +L Sbjct: 189 PFLLGGIIGVVGFWLRRNIDEPEEYKQ---ARQASKASKIKKNPLIA--AIRCGGLRGML 243 Query: 263 TCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRF 322 + +V Y+LL +M ++L ++ +I + + P+ GLLSDRF Sbjct: 244 HVFMVQPVFSVGAYLLLGFMYTFLIEVGKLDSTSALISNAIAVIVLSALLPLGGLLSDRF 303 Query: 323 GRRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPT 382 GR+ + G+ + + A PA L S AG +LA L + FPT Sbjct: 304 GRKRVLTFGAAWIALSAYPAMYLAASGSFASAVAGQTLLAAGLGIYGAASFVAAAEFFPT 363 Query: 383 HIRYSALAAAFNISV-LVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKET 441 R + A ++ SV + G P +AA+L ++ + + PA+Y+ ++AV+ LIT + ET Sbjct: 364 SFRATGHAISYQTSVAMFGGTCPLIAAYLSQAFGSPLAPAFYVTLIAVLCLITTQFVPET 423 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: 574 Number of extensions: 33 Number of successful extensions: 6 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: 500 Length of database: 456 Length adjustment: 34 Effective length of query: 466 Effective length of database: 422 Effective search space: 196652 Effective search space used: 196652 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: 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