Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate 6936303 Sama_0492 sodium/proline symporter (RefSeq)
Query= SwissProt::P07117 (502 letters) >FitnessBrowser__SB2B:6936303 Length = 498 Score = 447 bits (1149), Expect = e-130 Identities = 238/486 (48%), Positives = 316/486 (65%), Gaps = 15/486 (3%) Query: 9 VTFCVYIFGMILIGFIAWR-STKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPGA 67 ++ +Y M+ IG A+R ST + Y+LGGR + P VTALSAGASDMSGW+LMGLPGA Sbjct: 7 ISLALYFIAMLAIGLFAYRNSTDDLAGYMLGGRQVSPHVTALSAGASDMSGWMLMGLPGA 66 Query: 68 VFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILRI 127 +F G WIA GL LGA +N+ LVA RLRV TE ++ALTLPD+F+ RF + +R+ Sbjct: 67 MFTMGYDALWIAAGLLLGALLNYLLVAPRLRVFTEAADDALTLPDFFSKRFNKDNGSVRM 126 Query: 128 ISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWTD 187 ISA VI+LFFT+Y ++G+VAG + FES FG+ Y+T L + + YT +GGFLAVS TD Sbjct: 127 ISAAVIILFFTLYTSAGLVAGGKFFESAFGLGYQTGLLLTVSVVVAYTLLGGFLAVSLTD 186 Query: 188 TVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIISLMGWGLG 247 VQ +M AL+L P++ + D L + D + + +AI+S + WGLG Sbjct: 187 FVQGCIMFLALVLVPLVALQEFNSSTDMLAQASRSITPLADSFEHMGILAIVSSLAWGLG 246 Query: 248 YFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFND-HPALAGAV 306 YFGQPHI+ RFMA S I AR I M+WM++ + GA+A G G+AY N P L Sbjct: 247 YFGQPHIIVRFMAIRSVKDIAVARNIGMSWMLVTILGALATGLIGVAYVNKFKPGL---- 302 Query: 307 NQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAFLRKHA 366 + E +FI A+ILF+P I+G LL+AILAA+MST+S QLLV SS+++ED+Y+A K Sbjct: 303 -DDGETIFILFAEILFHPLISGFLLAAILAAIMSTISSQLLVSSSSLSEDVYRALFHKEM 361 Query: 367 SQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVMWSRMT 426 QK V GR+ VL VA VA LA + +L LVS AWAGFGAAFGP+VL S+ W RMT Sbjct: 362 DQKATVTAGRIGVLAVAAVATLLALDNNASILSLVSNAWAGFGAAFGPLVLLSLFWPRMT 421 Query: 427 RNGALAGMIIGALTVIVWKQFGWLG--------LYEIIPGFIFGSIGIVVFSLLGKAPSA 478 +GA+AG++ GA TV+VW Q L +YEI+PGFI ++ IV+ S +AP Sbjct: 422 HSGAVAGILCGAGTVLVWSQVPLLENGLPLSSLIYEIVPGFIVSTLAIVLVSYADQAPCK 481 Query: 479 AMQKRF 484 + QK F Sbjct: 482 STQKAF 487 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: 643 Number of extensions: 30 Number of successful extensions: 3 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: 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