Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate 370215 SO3097.4 hypothetical sodium/proline symporter (NCBI ptt file)
Query= SwissProt::P07117 (502 letters) >FitnessBrowser__MR1:370215 Length = 246 Score = 199 bits (507), Expect = 7e-56 Identities = 116/267 (43%), Positives = 158/267 (59%), Gaps = 28/267 (10%) Query: 183 VSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVD--MLKGLN----FV 236 +SWTD QASLM+ AL++ P V IE++D ML ++ + Sbjct: 1 MSWTDFFQASLMLIALLIIPFAVFSRPESHA---------GIESIDPAMLALISDKTTMI 51 Query: 237 AIISLMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYF 296 ++SL+ WGLGYFGQPHIL+RFMA + ++ +RRI+M+WMIL L GA+A G G YF Sbjct: 52 GLLSLLAWGLGYFGQPHILSRFMAIGTVDALPTSRRIAMSWMILSLLGALATGLAGSVYF 111 Query: 297 NDHPALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITED 356 + P NAE VF LAQ FNPWI G+L++AIL+A+MST+ QLLVCSS ITED Sbjct: 112 ANEPL------ANAETVFFHLAQAAFNPWIGGLLIAAILSAIMSTIDSQLLVCSSVITED 165 Query: 357 LYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVV 416 Y+ +LR +EL+ VGR+ VL +A++A +A NPEN VL LVSYAW G Sbjct: 166 FYRKWLRP-TDDRELMMVGRMGVLAIAVIAGIIALNPENSVLNLVSYAWQDLAPLSGQSY 224 Query: 417 LFSVMWSRMTRNGALAGMIIGALTVIV 443 + S +A M++ ++V Sbjct: 225 FYRCFGSN------IAAMVLSQALLLV 245 Lambda K H 0.328 0.140 0.436 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: 314 Number of extensions: 16 Number of successful extensions: 4 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: 502 Length of database: 246 Length adjustment: 29 Effective length of query: 473 Effective length of database: 217 Effective search space: 102641 Effective search space used: 102641 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 (21.8 bits) S2: 49 (23.5 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