Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_008539556.1 HMPREF9454_RS09855 sodium/proline symporter PutP
Query= SwissProt::P07117 (502 letters) >NCBI__GCF_000245775.1:WP_008539556.1 Length = 501 Score = 483 bits (1244), Expect = e-141 Identities = 245/494 (49%), Positives = 330/494 (66%), Gaps = 25/494 (5%) Query: 1 MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60 M+ + ++V F +Y+ M+ IG + T N DYILGGR LG +VT++SA ASDMSGW+ Sbjct: 1 MSDNISIIVAFLLYLLFMMAIGVYFYYRTHNMSDYILGGRKLGAWVTSMSAEASDMSGWM 60 Query: 61 LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120 LMGLPG +L+G++ WIA+GL LG W NW+ +A RLR +TE NN+LTLPD+ R+ D Sbjct: 61 LMGLPGFAYLAGLNAGWIAVGLALGTWANWQFIARRLRKYTELANNSLTLPDFLQNRYHD 120 Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180 KS ++R++ A+ IL+FF IY +SG VAG +LF + FG+ YE AL GA + YTF+GGF Sbjct: 121 KSPLIRVVMAIFILIFFIIYTSSGFVAGGKLFNTIFGIPYEYALCLGAFVIVFYTFVGGF 180 Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGL------- 233 LAV WTD +Q +M FA+++ P+ ++GGFGD+ I SI N + Sbjct: 181 LAVCWTDFIQGVMMFFAILIVPIAAAFTLGGFGDTYTAI---SITNPEFFNPFTKSDGSY 237 Query: 234 -NFVAIISLMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFG 292 + +ISL+ WGLGYFGQPHIL RFMA S + A RI+MTW+++ L AV VG G Sbjct: 238 TTVLELISLLAWGLGYFGQPHILVRFMAITSSSELKKATRIAMTWVVISLTAAVCVGMVG 297 Query: 293 IAYFNDHPALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSA 352 Y L G N+E VF+ + LF+P+ AGI+LSA+LAA+MST S QLLV +SA Sbjct: 298 SVYLT--TPLNGT---NSETVFLVMTDHLFSPFWAGIVLSAVLAAIMSTASAQLLVGASA 352 Query: 353 ITEDLYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAF 412 + +DLYK F+ K + +ELV V R+ V+ +AL+AIAL +P N +L +V+YAWAGFGA F Sbjct: 353 VAQDLYKQFIHKDINPRELVLVTRLSVIGIALIAIALGLDPNNSILNIVAYAWAGFGATF 412 Query: 413 GPVVLFSVMWSRMTRNGALAGMIIGALTVIVWKQ---------FGWLGLYEIIPGFIFGS 463 GP +LFS+ W R TRNG LAGMI+G +TV+VWKQ + L LYEI+PGFI S Sbjct: 413 GPALLFSLFWRRTTRNGILAGMIVGGITVLVWKQITLLDIATVYPILQLYEIVPGFILSS 472 Query: 464 IGIVVFSLLGKAPS 477 + I++ S L KAPS Sbjct: 473 LAIIIGSKLDKAPS 486 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: 708 Number of extensions: 38 Number of successful extensions: 4 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: 501 Length adjustment: 34 Effective length of query: 468 Effective length of database: 467 Effective search space: 218556 Effective search space used: 218556 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