Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate 7026926 Shewana3_4055 sodium/proline symporter (RefSeq)
Query= SwissProt::P07117 (502 letters) >FitnessBrowser__ANA3:7026926 Length = 498 Score = 425 bits (1093), Expect = e-123 Identities = 229/488 (46%), Positives = 314/488 (64%), Gaps = 13/488 (2%) Query: 9 VTFCVYIFGMILIGFIAWR-STKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPGA 67 V+ +Y M+ IG A+R ST + YILGGR + P VTALSAGASDMSGW+LMGLPGA Sbjct: 7 VSLAIYFIAMLAIGLFAYRKSTDDVSGYILGGRQVSPHVTALSAGASDMSGWMLMGLPGA 66 Query: 68 VFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILRI 127 +FL G +IA+GL +GA IN+ +VA +LRV+TE +NALT+P++F RF +RI Sbjct: 67 MFLVGFETLYIALGLLIGALINYLVVAPKLRVYTEVADNALTIPEFFAKRFGQADNSIRI 126 Query: 128 ISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWTD 187 I+A +I++FFT+Y ++G+VAG +LFES FG++Y+ L A + YT +GGFLAVS TD Sbjct: 127 IAAAIIVIFFTLYTSAGLVAGGKLFESAFGLNYDIGLVVTLAVVVSYTLLGGFLAVSLTD 186 Query: 188 TVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIISLMGWGLG 247 VQ +M AL+L P + + Q D ++ + + +IS + WGLG Sbjct: 187 FVQGCIMFVALVLVPFVAYQEFTSADRMMNFAYQSIPHFTDAMQNVTLLGLISSLSWGLG 246 Query: 248 YFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPALAGAVN 307 YFGQPHI+ RFMA S I ARRI ++WM + + GA+A G GIAY N G Sbjct: 247 YFGQPHIIVRFMAIRSVADIKTARRIGISWMTVTIIGALATGLVGIAYANKF----GMKL 302 Query: 308 QNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAFLRKHAS 367 + E +FI +++LF+P I+G LL+AILAA+MST+S QLLV SS++TED+Y+ +K AS Sbjct: 303 SDPETIFIVFSELLFHPLISGFLLAAILAAIMSTISSQLLVSSSSLTEDIYRTLSKKQAS 362 Query: 368 QKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVMWSRMTR 427 ++E+V +GR V VA+VA LA + N +L LVS AWAGFGAAFGP+VLFS+ + +T Sbjct: 363 EQEMVKMGRYGVAGVAIVATLLALDRSNSILSLVSNAWAGFGAAFGPLVLFSLYKANLTH 422 Query: 428 NGALAGMIIGALTVIVWKQFGWLG--------LYEIIPGFIFGSIGIVVFSLLGKAPSAA 479 A+AG+I GALTV+ W L +YE+IPGF+ S I + S P A Sbjct: 423 KAAIAGIISGALTVLFWIYAPVLSDGKALSSLVYEMIPGFVVSSTVIYLVSKFDNDPCAK 482 Query: 480 MQKRFAEA 487 K+F +A Sbjct: 483 TTKQFHQA 490 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: 685 Number of extensions: 36 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 502 Length of database: 498 Length adjustment: 34 Effective length of query: 468 Effective length of database: 464 Effective search space: 217152 Effective search space used: 217152 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