Align proline porter II (characterized)
to candidate N515DRAFT_3073 N515DRAFT_3073 Arabinose efflux permease
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Dyella79:N515DRAFT_3073 Length = 551 Score = 210 bits (534), Expect = 1e-58 Identities = 122/325 (37%), Positives = 180/325 (55%), Gaps = 16/325 (4%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 R+ I A+SLG EW+DF +YG +A +GK FF G + + + AL F+ F +RP G Sbjct: 16 RRVILASSLGTVFEWYDFYLYGSLAVLIGKHFFSGLNETSAFIFALLAFAAGFAVRPFGA 75 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 + FG LGD GR+ ITI+IM +STF +G++PSY T+G+ AP+LL++ ++ QG ++GG Sbjct: 76 IVFGRLGDLVGRKYTFLITIIIMGLSTFLVGVLPSYSTVGMIAPVLLIVLRLLQGLALGG 135 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 EY GA+ +VAE++PD KRG S++ + G L V++ +G+ F DWGWRIP Sbjct: 136 EYGGAATYVAEHAPDGKRGLYTSFIQITATFGLFLSLLVILGTRMALGDKVFEDWGWRIP 195 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSL-- 261 F I+ L + +Y+R L+E+P FQQ EG K E A +W++L Sbjct: 196 FLISSVLVAVSVYIRLQLQESPVFQQM-------KAEGKHS--KAPLTE-AFGHWKNLKV 245 Query: 262 --LTCIGLVIATNVTYYMLLTYMPSYLSHNLHY-SEDHGVLIIIAIMIGMLFVQPVMGLL 318 L +G V +Y Y +L+ +L +LI A++IG F G L Sbjct: 246 VILALLGATAGQAVVWYTGQFYALYFLTQSLKIDGTTANLLIAAALIIGTPFF-VFFGWL 304 Query: 319 SDRFGRRPFVLLGSVALFVLAIPAF 343 SDR GR+ VL G + + P F Sbjct: 305 SDRIGRKSIVLAGCLLAALTYFPIF 329 Score = 39.7 bits (91), Expect = 3e-07 Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 2/86 (2%) Query: 358 LLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLVESSQN 416 L +L + + G +A+ L MFPT IRY++++ ++I + G PT+ LV + Sbjct: 459 LAILVLYVTMVYGPIAAWLVEMFPTRIRYTSMSLPYHIGNGWFGGFVPTIGFMLVAWKGD 518 Query: 417 LMMPAYYLMVVAVVGLITGVT-MKET 441 + +Y ++VAV G+ +KET Sbjct: 519 IYYGLWYPIIVAVGTFFIGLLFLKET 544 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: 711 Number of extensions: 45 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 551 Length adjustment: 35 Effective length of query: 465 Effective length of database: 516 Effective search space: 239940 Effective search space used: 239940 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