Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_109968238.1 DK846_RS07180 sodium/proline symporter PutP
Query= SwissProt::P07117 (502 letters) >NCBI__GCF_003173355.1:WP_109968238.1 Length = 496 Score = 471 bits (1211), Expect = e-137 Identities = 237/487 (48%), Positives = 328/487 (67%), Gaps = 10/487 (2%) Query: 7 MLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLMGLPG 66 ++ F VY+ M+ IG + +R T N DYILG R L +V +LSA ASDMSGWLL+GLPG Sbjct: 8 IITAFVVYLAVMLSIGALYYRKTHNVSDYILGSRGLNKYVASLSAEASDMSGWLLIGLPG 67 Query: 67 AVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKSRILR 126 ++SG+ W+A+GL LG ++NWKLVA RLR++T+ ++LTLP++F RFEDKS I+ Sbjct: 68 LAYVSGMQAGWVALGLILGTFLNWKLVAKRLRIYTQSAGDSLTLPEFFKNRFEDKSDIIG 127 Query: 127 IISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLAVSWT 186 I A+ IL+FF +Y ++ V+ +LF + FG+ Y TAL G+ ++YTFIGGF+AV WT Sbjct: 128 GICAIFILIFFLLYTSAQFVSTGKLFNTVFGIDYTTALLIGSLIVVVYTFIGGFMAVCWT 187 Query: 187 DTVQASLMIFALILTPVIVIISVGG---FGDSLEVIKQKSIENVDMLKG--LNFVAIISL 241 D Q LM+FA+++ P+ + +GG DS+ + + + G L +AIISL Sbjct: 188 DFFQGLLMLFAILVVPIAAVGLLGGPVATIDSINAVNPNLLNPFTGVDGTPLTAIAIISL 247 Query: 242 MGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPA 301 M WGLGYFGQPHIL RFMA I HAR ++M W+IL L AVA+G G F P Sbjct: 248 MAWGLGYFGQPHILVRFMAIRDPKEIAHARTVAMIWVILSLTAAVAIGLVG-KVFLSQPL 306 Query: 302 LAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKAF 361 + A +E VF+ + +F ++AGI+L ILAA+MST S QLLV SSA++EDLY+ + Sbjct: 307 VGSA----SETVFMVMTDQIFFSFLAGIILCGILAAIMSTASSQLLVTSSAVSEDLYRTY 362 Query: 362 LRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSVM 421 LR HAS+KE +WV R+ VLV A++AI L NP++ V G+VSYAWAGFGAAFGP +L ++ Sbjct: 363 LRPHASEKEGIWVSRISVLVAAIIAIILGLNPDSLVYGIVSYAWAGFGAAFGPALLMALF 422 Query: 422 WSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAMQ 481 W RMT+ GALAG+I G +TV++WKQ GLYEI+PGFI + I V S++ AP +++ Sbjct: 423 WRRMTKAGALAGIISGGVTVLIWKQLNLFGLYEIVPGFIIALVAIYVVSIITPAPDSSIV 482 Query: 482 KRFAEAD 488 F + + Sbjct: 483 TVFDDVE 489 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: 724 Number of extensions: 43 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: 496 Length adjustment: 34 Effective length of query: 468 Effective length of database: 462 Effective search space: 216216 Effective search space used: 216216 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