Align Sodium-dependent proline transporter (Solute carrier family 6 member 7) (characterized)
to candidate 5210455 Shew_2896 sodium:neurotransmitter symporter (RefSeq)
Query= TCDB::Q99884 (636 letters) >FitnessBrowser__PV4:5210455 Length = 503 Score = 244 bits (622), Expect = 9e-69 Identities = 156/529 (29%), Positives = 261/529 (49%), Gaps = 56/529 (10%) Query: 37 RGNWTGKLDFLLSCIGYCVGLGNVWRFPYRAYTNGGGAFLVPYFLMLAICGIPLFFLELS 96 R W ++ F+L+ +G +GLGN+WRFPY AY NGGGAF +PY + GIP +E S Sbjct: 3 REQWNSRVGFILAAVGSAIGLGNIWRFPYMAYDNGGGAFFIPYLFAMITAGIPFMIMEFS 62 Query: 97 LGQ---------FSSLGPLAVWKISPLFKGAGAAMLLIVGLVAIYYNMIIAYVLFYLFAS 147 LG F+ LG +++ L G + I ++A+YY II + L YL S Sbjct: 63 LGHKIKKTSPRIFAQLGHTLGFRLEWL----GWFQVFIAAVIAVYYVAIIGWTLSYLGFS 118 Query: 148 LTSDLPWEHCGNWWNTELCLEHRVSKDGNGALPLNLTCTVSPSEEYWSRYVLHIQGSQGI 207 + W +P++ +++ Y+ G+ Sbjct: 119 FSQA---------WGD------------------------NPNDFFFNHYLK--LGNNSP 143 Query: 208 GSPGEIRWNLCLCLLLAWVIVFLCILKGVKSS-GKVVYFTATFPYLILLMLLVRGVTLPG 266 GE + + + + +AW++ F+ + GVK + ++++L+L+ R + LPG Sbjct: 144 SHLGEFQIGIAIAMSIAWLMTFMAVFTGVKGGIERANKIMMPMLFIMVLVLIGRIMFLPG 203 Query: 267 AWKGIQFYLTPQFHHLLSSKVWIEAALQIFYSLGVGFGGLLTFASYNTFHQNIYRDTFIV 326 A G+ + P F LL ++VW A QIF++L VGF +L ++SY +I + F+ Sbjct: 204 ALSGLNYLFEPDFSRLLDAQVWSAAYGQIFFTLSVGFAIMLAYSSYLPTKADINNNAFMT 263 Query: 327 TLGNAITSILAGFAIFSVLGYMSQELGVPVDQVAKAGPGLAFVVYPQAMTMLPLSPFWSF 386 L N SILAG IF VLGYM++E P+ +V +G GLAFV P A+ ++P Sbjct: 264 VLINCGFSILAGILIFGVLGYMAEEQMKPLTEVVSSGIGLAFVTIPTAINLMPAPYILGP 323 Query: 387 LFFFMLLTLGLDSQFAFLETIVTAVTDEFPYYLRPKKAVFSGLICVAMYLMGLILTTDGG 446 LFF L+ GL S + +E + +AV D+F ++R K A L+C YL+ + T+GG Sbjct: 324 LFFIALVIAGLSSHISIIEAVTSAVIDKF--HVRRKPAAV--LVCSLGYLVSMAFATNGG 379 Query: 447 MYWLVLLDDYSASFGLMVVVITTCLAVTRVYGIQRFCRDIHMMLGFKPGLYFRACWLFLS 506 + L L+D + + L++ + + +T + + + + F+ G +F C F+S Sbjct: 380 LLLLDLVDYFINNIALLLSCLLELVIITWLLKVTVIHQHANENSEFRVGGWFVVCLRFIS 439 Query: 507 PATLLALMVYSIVKYQPSEYGSYRFPPWAELLGILMGLLSCLMIPAGML 555 PA L ++ ++ + YG Y P A+ L + GL+ ++ A ++ Sbjct: 440 PAILATILAKNLYNTLVNGYGDY---PIADQLFLGWGLVGTMLFFAVLI 485 Lambda K H 0.327 0.143 0.459 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: 851 Number of extensions: 35 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: 2 Length of query: 636 Length of database: 503 Length adjustment: 36 Effective length of query: 600 Effective length of database: 467 Effective search space: 280200 Effective search space used: 280200 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 (21.7 bits) S2: 53 (25.0 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