Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate 6938044 Sama_2177 sodium/proline symporter (RefSeq)
Query= SwissProt::P07117 (502 letters) >FitnessBrowser__SB2B:6938044 Length = 482 Score = 506 bits (1303), Expect = e-148 Identities = 259/478 (54%), Positives = 340/478 (71%), Gaps = 14/478 (2%) Query: 1 MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60 M+I TP+LVTF Y+ M+ IGF A+++T + DDYILGGR +GP VTALS GASDMSGWL Sbjct: 1 MSIDTPILVTFVGYLALMMGIGFWAYKATDSVDDYILGGRKMGPGVTALSVGASDMSGWL 60 Query: 61 LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120 L+GLPGAV+L G+ E+WI IGL +GAW+NW VA RLR++T+ +NALTLPD+F RF D Sbjct: 61 LLGLPGAVYLGGLGEAWIGIGLVIGAWLNWLFVAKRLRIYTQLADNALTLPDFFEKRFHD 120 Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180 K+ +LR +SAL IL+FFT Y +SG+V GA LFE FG+ Y AL G+A + YTF+GGF Sbjct: 121 KAGLLRFVSALTILVFFTFYASSGMVGGAILFEKVFGLDYTAALVIGSAIIVGYTFVGGF 180 Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDML-KGLNFVAII 239 AVSWTD Q LM+ AL++ P+ + + +S I S E + ++ +G + + Sbjct: 181 FAVSWTDFFQGCLMLIALLIVPMAIFTN----SESHASIDTLSPEMLSLIGEGTTLMGVA 236 Query: 240 SLMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDH 299 SLM WGLGYFGQPHIL+RFMA + + +RRI+M+WMI+ L GA+A G G YF Sbjct: 237 SLMAWGLGYFGQPHILSRFMAIERPEHLPVSRRIAMSWMIVSLMGALATGLAGSLYFAKE 296 Query: 300 PALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYK 359 P NAE VFI LAQ+ FNPWIAG+L++AIL+A+MST+ QLLVCSS +TED Y+ Sbjct: 297 PL------ANAETVFIHLAQVAFNPWIAGLLIAAILSAIMSTIDSQLLVCSSVVTEDFYR 350 Query: 360 AFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFS 419 LR A EL+ VGR+ VL +A++A +A +P++ VLGLVSYAWAGFGAAFGPVVL S Sbjct: 351 K-LRPKADDNELMRVGRIGVLAIAIIAGVVALDPQSSVLGLVSYAWAGFGAAFGPVVLLS 409 Query: 420 VMWSRMTRNGALAGMIIGALTVIVWKQF--GWLGLYEIIPGFIFGSIGIVVFSLLGKA 475 + W ++ GALA +I GA+TV+VWKQ G+ LYEI+PGFI ++ V+ SL+ A Sbjct: 410 LFWRGYSKTGALATIITGAVTVVVWKQLSGGFFDLYEILPGFILATLAGVLISLVAPA 467 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: 775 Number of extensions: 37 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: 482 Length adjustment: 34 Effective length of query: 468 Effective length of database: 448 Effective search space: 209664 Effective search space used: 209664 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: 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