Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate 5210585 Shew_3013 sodium/proline symporter (RefSeq)
Query= SwissProt::P07117 (502 letters) >FitnessBrowser__PV4:5210585 Length = 498 Score = 415 bits (1067), Expect = e-120 Identities = 231/489 (47%), Positives = 314/489 (64%), Gaps = 15/489 (3%) Query: 9 VTFCVYIFGMILIGFIAWR-STKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPGA 67 ++ +Y M+ IG A+R ST + YILGGR + P VTALSAGASDMSGW+LMGLPGA Sbjct: 7 ISLAIYFLAMLAIGLFAYRRSTDDVSGYILGGRQVSPQVTALSAGASDMSGWMLMGLPGA 66 Query: 68 VFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILRI 127 +FL G +IA+GL LGA +N+ +VA +LRV+TE NNALT+P++F RF D S +RI Sbjct: 67 MFLVGFETIYIALGLLLGALVNYLIVAPKLRVYTEVANNALTIPEFFAKRFHDPSCNVRI 126 Query: 128 ISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWTD 187 ISA +I++FFT+Y ++G+VAG +LFES F ++YE L + YT +GGFLAVS TD Sbjct: 127 ISAAIIVIFFTLYTSAGLVAGGKLFESAFEVNYELGLVITLGVVVSYTLLGGFLAVSLTD 186 Query: 188 TVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENV-DMLKGLNFVAIISLMGWGL 246 VQ +M ALIL PV+ D + +SI + + ++ + + +IS + WGL Sbjct: 187 FVQGCIMFVALILVPVVAYQEFSN-ADKMMNFAYESIPHFGEAMQNVTLLGLISALSWGL 245 Query: 247 GYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPALAGAV 306 GYFGQPHI+ RFMA S I A+ I M+WM + + GA+A G GIAY N Sbjct: 246 GYFGQPHIIVRFMAIRSVSDIKTAKNIGMSWMTVTIIGALATGLVGIAYANKFDMKL--- 302 Query: 307 NQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAFLRKHA 366 + E +FI +++LF+P I+G LL+AILAA+MST+S QLLV SS++TED+Y+ +K A Sbjct: 303 -SDPETIFIVFSELLFHPLISGFLLAAILAAIMSTISSQLLVSSSSLTEDIYRVVSKKEA 361 Query: 367 SQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVMWSRMT 426 S++E+V +GR V VA+VA LA + N +L LVS AWAGFGAAFGP+VLFS+ +T Sbjct: 362 SEEEMVKLGRFGVAGVAIVASLLALDRSNSILSLVSNAWAGFGAAFGPLVLFSLYKKNLT 421 Query: 427 RNGALAGMIIGALTVIVWKQFGWLG--------LYEIIPGFIFGSIGIVVFSLLGKAPSA 478 A+AG++ GA TV+ W L LYE+IPGF+ S+ I S L P Sbjct: 422 HKAAVAGIVAGAATVLFWIYAPVLPEGKALSSMLYEMIPGFMASSLVIWGVSALDGDPCE 481 Query: 479 AMQKRFAEA 487 + F EA Sbjct: 482 NTIETFDEA 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: 704 Number of extensions: 34 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: 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