Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_084935516.1 HA51_RS15470 sodium/proline symporter PutP
Query= SwissProt::P07117 (502 letters) >NCBI__GCF_002095475.1:WP_084935516.1 Length = 494 Score = 831 bits (2146), Expect = 0.0 Identities = 407/493 (82%), Positives = 456/493 (92%) Query: 1 MAISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWL 60 M++STPMLVTF +YI GM+LIGF+A+RSTK+FDDYILGGRSLG VTALSAGASDMSGWL Sbjct: 1 MSVSTPMLVTFVIYILGMVLIGFVAYRSTKSFDDYILGGRSLGSVVTALSAGASDMSGWL 60 Query: 61 LMGLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFED 120 LMGLPGA+FLSGISESWIAIGLT+GAW+NWK+VAGRLRV TE+++NALTLPD+F+ RFED Sbjct: 61 LMGLPGAIFLSGISESWIAIGLTIGAWLNWKIVAGRLRVQTEHHDNALTLPDFFSSRFED 120 Query: 121 KSRILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGF 180 KS++LR+ISA+VIL+FFTIYCASG+VAGARLFESTFGM Y+TALWAGAAATILYT +GGF Sbjct: 121 KSKLLRVISAVVILIFFTIYCASGVVAGARLFESTFGMDYQTALWAGAAATILYTLVGGF 180 Query: 181 LAVSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIIS 240 LAVSWTDTVQASLMIFALILTPV VII+VGG DSL VI+ KS+EN+DMLKGLNFVA+IS Sbjct: 181 LAVSWTDTVQASLMIFALILTPVFVIIAVGGLDDSLAVIEAKSLENLDMLKGLNFVAVIS 240 Query: 241 LMGWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHP 300 L+GWGLGYFGQPHILARFMAADSH SI ARRI MTWMILCLAGAVAVGFFGIA+F +HP Sbjct: 241 LLGWGLGYFGQPHILARFMAADSHRSIRAARRIGMTWMILCLAGAVAVGFFGIAFFQNHP 300 Query: 301 ALAGAVNQNAERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLLVCSSAITEDLYKA 360 LA V+QN ERVFIELA+ILFNPWIAGILLSAILAAVMSTLSCQLLVCSSA+TEDLYK Sbjct: 301 ELAAGVSQNGERVFIELARILFNPWIAGILLSAILAAVMSTLSCQLLVCSSALTEDLYKG 360 Query: 361 FLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFSV 420 FLRK+ASQKELVWVGR+MVLV+AL+AIALAANPENRVLGLVSYAWAGFGAAFGPVVLF V Sbjct: 361 FLRKNASQKELVWVGRLMVLVIALIAIALAANPENRVLGLVSYAWAGFGAAFGPVVLFGV 420 Query: 421 MWSRMTRNGALAGMIIGALTVIVWKQFGWLGLYEIIPGFIFGSIGIVVFSLLGKAPSAAM 480 W RMTRNGALAGM+IGA+TV++WKQ+G++ LYEIIPGFIF SI IVVFSL+G PS A Sbjct: 421 CWKRMTRNGALAGMVIGAMTVLLWKQYGYVELYEIIPGFIFASIAIVVFSLIGNGPSEAA 480 Query: 481 QKRFAEADAHYHS 493 Q RFA A+A Y + Sbjct: 481 QARFAAAEAEYQT 493 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: 934 Number of extensions: 42 Number of successful extensions: 1 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 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