Align proline porter II (characterized)
to candidate SMc04407 SMc04407 transport transmembrane protein
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Smeli:SMc04407 Length = 629 Score = 202 bits (513), Expect = 4e-56 Identities = 112/328 (34%), Positives = 183/328 (55%), Gaps = 16/328 (4%) Query: 21 GKLRKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRP 80 G+ +K I A+SLG EW+DF +YG +A +G FF + + + AL F+ FL+RP Sbjct: 17 GEEKKVIFASSLGTVFEWYDFYLYGSLAVYIGATFFSQYPETTRNIFALLAFAAGFLVRP 76 Query: 81 LGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFS 140 G L FG LGD GR+ +TI+IM +STF +G++P +IGI API+L+ ++ QG + Sbjct: 77 FGALVFGRLGDLVGRKYTFLVTILIMGVSTFLVGVLPGAASIGIAAPIILIALRLLQGLA 136 Query: 141 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGW 200 +GGEY GA+ +VAE++P +RG+ SW+ + G L V++L+ ++G+ F +WGW Sbjct: 137 LGGEYGGAATYVAEHAPHGRRGYFTSWIQTTATLGLFLSLVVILLVQYMLGKEAFAEWGW 196 Query: 201 RIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWR- 259 RIPF ++ L + +++R + E+PAF++ E+G G K E A WR Sbjct: 197 RIPFLLSFVLLGVSVWIRLKMNESPAFKK---MKEEG------KGSKAPLTE-AFGQWRN 246 Query: 260 ---SLLTCIGLVIATNVTYYMLLTYMPSYLSHNLHY-SEDHGVLIIIAIMIGMLFVQPVM 315 ++L G V+ V +Y Y +L L + +++ ++++G F Sbjct: 247 AKIAVLALFGAVVGQAVVWYSGQFYALFFLQSILKVDGQSANLMVAASLLLGTGFF-VFF 305 Query: 316 GLLSDRFGRRPFVLLGSVALFVLAIPAF 343 G LSD+ GR+P ++ G + + P F Sbjct: 306 GWLSDKIGRKPIIMAGLLLAMLTYFPLF 333 Score = 39.7 bits (91), Expect = 3e-07 Identities = 26/96 (27%), Positives = 51/96 (53%), Gaps = 2/96 (2%) Query: 353 LIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLV 411 +I A L +L + + G +A+ L +FPT IRY+ ++ ++I + GL P A + Sbjct: 530 VIIAVLTVLVIYVTMVYGPIAALLVELFPTRIRYTGMSLPYHIGNGWFGGLLPATAFAMS 589 Query: 412 ESSQNLMMPAYYLMVVAVVGLITGVT-MKETANRPL 446 + ++ +Y +V A + L+ G+ + ET +R + Sbjct: 590 AAKGDIYYGLWYPIVFAGITLVIGLLFLPETKDRDI 625 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: 782 Number of extensions: 41 Number of successful extensions: 4 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: 629 Length adjustment: 36 Effective length of query: 464 Effective length of database: 593 Effective search space: 275152 Effective search space used: 275152 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: 53 (25.0 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