Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate PP_4946 PP_4946 sodium/L-proline transporter
Query= SwissProt::P07117 (502 letters) >FitnessBrowser__Putida:PP_4946 Length = 542 Score = 759 bits (1960), Expect = 0.0 Identities = 378/491 (76%), Positives = 426/491 (86%), Gaps = 1/491 (0%) Query: 3 ISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLM 62 + P+ +TF +YI M+LIGF A+R+T N DYILGGRSLG VTALSAGASDMSGWLLM Sbjct: 51 MGNPLTITFVIYIAAMVLIGFAAYRATNNLSDYILGGRSLGSVVTALSAGASDMSGWLLM 110 Query: 63 GLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKS 122 GLPGA++ +G+SE+WIAIGLT+GA++NW VAGRLRV TE+N +ALTLPDYF+ RFED S Sbjct: 111 GLPGAIYFAGLSEAWIAIGLTVGAYLNWLFVAGRLRVQTEHNGDALTLPDYFSSRFEDNS 170 Query: 123 RILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLA 182 +LRIISA+VIL+FFTIYCASGIVAGARLFESTFGMSYETALWAGAAATI YTF+GGFLA Sbjct: 171 GLLRIISAIVILVFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATIAYTFVGGFLA 230 Query: 183 VSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIISLM 242 VSWTDTVQASLMIFALILTPVIV+IS GGF + I+ + N DMLKG F+ IISLM Sbjct: 231 VSWTDTVQASLMIFALILTPVIVLISTGGFDQTFAAIEAVNPANFDMLKGATFIGIISLM 290 Query: 243 GWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPAL 302 GWGLGYFGQPHILARFMAADS SI ARRISMTWMILCLAG AVGFFGIAYF+ HP L Sbjct: 291 GWGLGYFGQPHILARFMAADSVKSIAKARRISMTWMILCLAGTCAVGFFGIAYFSAHPEL 350 Query: 303 AGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAFL 362 AG V++N ERVFIELA+ILFNPW+AG+LLSAILAAVMSTLSCQLLVCSSA+TED YKAFL Sbjct: 351 AGPVSENHERVFIELAKILFNPWVAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKAFL 410 Query: 363 RKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVMW 422 RK+ASQ ELVWVGR+MVL VAL+AIA+AANPENRVLGLV+YAWAGFGAAFGPVVL SV+W Sbjct: 411 RKNASQVELVWVGRLMVLAVALIAIAMAANPENRVLGLVAYAWAGFGAAFGPVVLISVLW 470 Query: 423 SRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAMQK 482 MTRNGALAG+++GALTVI+WK F LGLYEIIPGF+F SI IV+ S LG +PS M K Sbjct: 471 KGMTRNGALAGIVVGALTVILWKNFDTLGLYEIIPGFLFASIAIVLVSKLG-SPSQTMVK 529 Query: 483 RFAEADAHYHS 493 RF ADA YH+ Sbjct: 530 RFEAADAAYHA 540 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: 948 Number of extensions: 50 Number of successful extensions: 3 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: 542 Length adjustment: 35 Effective length of query: 467 Effective length of database: 507 Effective search space: 236769 Effective search space used: 236769 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