Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_090274945.1 BLU11_RS15570 sodium/proline symporter PutP
Query= SwissProt::P07117 (502 letters) >NCBI__GCF_900105005.1:WP_090274945.1 Length = 500 Score = 460 bits (1183), Expect = e-134 Identities = 237/482 (49%), Positives = 325/482 (67%), Gaps = 18/482 (3%) Query: 8 LVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPGA 67 LV +Y M+ IG+ A+R T + DDY+L GR L P V ALSAGASDMSGWLLMGLPGA Sbjct: 8 LVAIGLYFLTMLGIGYYAYRQTTDLDDYMLAGRKLSPGVAALSAGASDMSGWLLMGLPGA 67 Query: 68 VFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILRI 127 ++ SG+ E+WIAIGLT+GA++NW+ VA RLR +TE +NN++T+P + RF+DK+R+LRI Sbjct: 68 IYASGLVEAWIAIGLTIGAYLNWRFVAPRLRSYTEVSNNSITVPSFMENRFKDKTRLLRI 127 Query: 128 ISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWTD 187 S ++IL+FFT Y +SG+VAG FE++F Y + + T+ YT GGFL S TD Sbjct: 128 ASGVIILVFFTFYVSSGMVAGGVFFEASFNTPYLFGMLLVSGITLTYTLFGGFLGASLTD 187 Query: 188 TVQASLMIFALILTPVIVIISVGGFGDSLEVIKQ-----------KSIENVDMLKGLNFV 236 VQ LM+ ALI+ PV+ +I +GG G++++ I + +L G + + Sbjct: 188 VVQGLLMLAALIIVPVLTVIGMGGLGETIDAIHAADAAHNLANPGDELHRTSLLFGGSLL 247 Query: 237 AIISLMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYF 296 AIIS WGLGYFGQPHI+ RFMA S RRI + WMIL +GAV G G+ YF Sbjct: 248 AIISAASWGLGYFGQPHIIVRFMALRSSADAKAGRRIGIGWMILVASGAVFTGLIGVGYF 307 Query: 297 NDHPALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITED 356 + + V N E VF+ L+QILF+P +AG++L+A+LAA+MST+S QL+VCSSA+ ED Sbjct: 308 H----TSNEVLDNPETVFLLLSQILFHPLVAGLVLAAVLAAIMSTVSSQLIVCSSALVED 363 Query: 357 LYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVV 416 LYK F K + + V +GR+ VL VA++A LA +P + +LGLV++AWAGFGAAFGP++ Sbjct: 364 LYKIF-GKDLTALQQVRLGRLGVLTVAVIAALLAIDPRSNILGLVAFAWAGFGAAFGPII 422 Query: 417 LFSVMWSRMTRNGALAGMIIGALTVIVWKQFGWLG--LYEIIPGFIFGSIGIVVFSLLGK 474 L S+ W ++T GALAGMI GA+ V +W L +YEI+PGF+ ++ +V SLL K Sbjct: 423 LLSLFWRKLTAMGALAGMITGAVVVGIWGNIASLQALMYEIVPGFLACTVVAIVVSLLIK 482 Query: 475 AP 476 P Sbjct: 483 TP 484 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: 747 Number of extensions: 51 Number of successful extensions: 5 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: 500 Length adjustment: 34 Effective length of query: 468 Effective length of database: 466 Effective search space: 218088 Effective search space used: 218088 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 24 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