Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate AO353_12815 AO353_12815 proline:sodium symporter PutP
Query= SwissProt::P07117 (502 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12815 Length = 494 Score = 751 bits (1939), Expect = 0.0 Identities = 374/492 (76%), Positives = 428/492 (86%), Gaps = 1/492 (0%) Query: 1 MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60 M+ S P L+TF +YI M+LIGF+A+RST N DYILGGRSLG VTALSAGASDMSGWL Sbjct: 1 MSASNPTLITFVIYIAAMVLIGFMAYRSTNNLSDYILGGRSLGSVVTALSAGASDMSGWL 60 Query: 61 LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120 LMGLPGA+++SG+SESWIAIGL +GA++NW VAGRLRV TE+N +ALTLPDYF+ RFED Sbjct: 61 LMGLPGAIYMSGLSESWIAIGLIVGAYLNWLFVAGRLRVQTEHNGDALTLPDYFSSRFED 120 Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180 KS +LRIISA+VIL+FFTIYCASGIVAGARLFESTFGMSYETALWAGAAATI YTF+GGF Sbjct: 121 KSGLLRIISAVVILVFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATIAYTFVGGF 180 Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIIS 240 LAVSWTDTVQA+LMIFAL+LTP+IV+++ GG + I+ + N DMLK +F+ IIS Sbjct: 181 LAVSWTDTVQATLMIFALLLTPIIVLLATGGIDTTFLAIEAQDPGNFDMLKNTSFIGIIS 240 Query: 241 LMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHP 300 LMGWGLGYFGQPHILARFMAADS SI +ARRISMTWMILCL G VAVGFFGIAYF+ +P Sbjct: 241 LMGWGLGYFGQPHILARFMAADSVKSIANARRISMTWMILCLGGTVAVGFFGIAYFSANP 300 Query: 301 ALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKA 360 A+A V++N ERVFIELA+ILFNPWIAG+LLSAILAAVMSTLSCQLLVCSSA+TED YK+ Sbjct: 301 AVAMPVSENHERVFIELAKILFNPWIAGVLLSAILAAVMSTLSCQLLVCSSALTEDFYKS 360 Query: 361 FLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSV 420 FLRK+ASQ ELVWVGR MVL VAL+AIALAANPENRVLGLVSYAWAGFGAAFGPVVL SV Sbjct: 361 FLRKNASQVELVWVGRAMVLAVALIAIALAANPENRVLGLVSYAWAGFGAAFGPVVLISV 420 Query: 421 MWSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAM 480 +W MTRNGALAG+++GALTVIVWK F LGLYEIIPGFIF S+ I++ S +G PSA M Sbjct: 421 LWKGMTRNGALAGIVVGALTVIVWKHFNLLGLYEIIPGFIFASLAILLVSKMG-VPSAGM 479 Query: 481 QKRFAEADAHYH 492 +RFA A+ +H Sbjct: 480 LQRFAAAEKDFH 491 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: 878 Number of extensions: 42 Number of successful extensions: 2 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: 494 Length adjustment: 34 Effective length of query: 468 Effective length of database: 460 Effective search space: 215280 Effective search space used: 215280 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