Align L-proline uptake porter, PutP (characterized)
to candidate 6938044 Sama_2177 sodium/proline symporter (RefSeq)
Query= TCDB::Q9I5F5 (506 letters) >FitnessBrowser__SB2B:6938044 Length = 482 Score = 512 bits (1319), Expect = e-149 Identities = 274/499 (54%), Positives = 351/499 (70%), Gaps = 26/499 (5%) Query: 1 MSVNTPTLITFVIYIAAMVLIGLAAYRSTNNFSDYILGGRSLGSFVTALSAGASDMSGWL 60 MS++TP L+TFV Y+A M+ IG AY++T++ DYILGGR +G VTALS GASDMSGWL Sbjct: 1 MSIDTPILVTFVGYLALMMGIGFWAYKATDSVDDYILGGRKMGPGVTALSVGASDMSGWL 60 Query: 61 LMGLPGAVYLSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGNALTLPDYFTNRFED 120 L+GLPGAVYL GL E+WI IGL++GA+LNWLFVA RLR+ T+ NALTLPD+F RF D Sbjct: 61 LLGLPGAVYLGGLGEAWIGIGLVIGAWLNWLFVAKRLRIYTQLADNALTLPDFFEKRFHD 120 Query: 121 NSRLLRIFSALVILVFFTIYCASGIVAGARLFESTFGLSYETALWAGAAATIAYTFIGGF 180 + LLR SAL ILVFFT Y +SG+V GA LFE FGL Y AL G+A + YTF+GGF Sbjct: 121 KAGLLRFVSALTILVFFTFYASSGMVGGAILFEKVFGLDYTAALVIGSAIIVGYTFVGGF 180 Query: 181 LAVSWTDTVQASLMIFALILTPVIVMLATGGVEPTFTAIELK---DATSFDML----KGA 233 AVSWTD Q LM+ AL++ P+ + FT E D S +ML +G Sbjct: 181 FAVSWTDFFQGCLMLIALLIVPMAI----------FTNSESHASIDTLSPEMLSLIGEGT 230 Query: 234 SFIGVISLMAWGLGYFGQPHILARFMAADSVKSIPAARRISMTWMILCLGGAVAVGFFGI 293 + +GV SLMAWGLGYFGQPHIL+RFMA + + +P +RRI+M+WMI+ L GA+A G G Sbjct: 231 TLMGVASLMAWGLGYFGQPHILSRFMAIERPEHLPVSRRIAMSWMIVSLMGALATGLAGS 290 Query: 294 AYFQAHPEQAGAVSENPERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSAL 353 YF P N E VFI LA++ FNPWIAG+L++AIL+A+MST+ QLLVCSS + Sbjct: 291 LYFAKEP------LANAETVFIHLAQVAFNPWIAGLLIAAILSAIMSTIDSQLLVCSSVV 344 Query: 354 TEDFYKAFLRKGASQLELVWVGRAMVLLVAVIAIWLASNPENRVLGLVSYAWAGFGAAFG 413 TEDFY+ LR A EL+ VGR VL +A+IA +A +P++ VLGLVSYAWAGFGAAFG Sbjct: 345 TEDFYRK-LRPKADDNELMRVGRIGVLAIAIIAGVVALDPQSSVLGLVSYAWAGFGAAFG 403 Query: 414 PLVLFSLLWKRMTRNGALAGMIVGAATVILWKNLL-GWTGLYEIIPGFLFASVAIVVFSL 472 P+VL SL W+ ++ GALA +I GA TV++WK L G+ LYEI+PGF+ A++A V+ SL Sbjct: 404 PVVLLSLFWRGYSKTGALATIITGAVTVVVWKQLSGGFFDLYEILPGFILATLAGVLISL 463 Query: 473 LGKAPSTSMLKRFDDAEQE 491 + A + S+ FD + + Sbjct: 464 VAPA-NDSVRAEFDSFQSK 481 Lambda K H 0.326 0.138 0.421 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: 835 Number of extensions: 41 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: 506 Length of database: 482 Length adjustment: 34 Effective length of query: 472 Effective length of database: 448 Effective search space: 211456 Effective search space used: 211456 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