Align Sodium/proline symporter; Proline permease; Propionate transporter (characterized)
to candidate WP_036832656.1 N784_RS04180 sodium/proline symporter PutP
Query= SwissProt::P07117 (502 letters) >NCBI__GCF_000775615.1:WP_036832656.1 Length = 505 Score = 554 bits (1427), Expect = e-162 Identities = 271/504 (53%), Positives = 368/504 (73%), Gaps = 17/504 (3%) Query: 3 ISTPMLVTFCVYIFGMILIGFIAWRSTKNFDDYILGGRSLGPFVTALSAGASDMSGWLLM 62 + T +VTF VY+ GM+ IG ++R T N DY+LGGR LGP V ALSAGASDMSGWLL+ Sbjct: 1 MGTATVVTFVVYLLGMLGIGIASYRLTSNLSDYVLGGRRLGPGVAALSAGASDMSGWLLL 60 Query: 63 GLPGAVFLSGISESWIAIGLTLGAWINWKLVAGRLRVHTEYNNNALTLPDYFTGRFEDKS 122 GLPGA++ SG+SE+WI IGL +GA++NW+ VA RLR +TE N+++T+PD+ RF D S Sbjct: 61 GLPGAIYASGLSEAWIGIGLAIGAYLNWQFVARRLRSYTEVANDSITVPDFLENRFRDNS 120 Query: 123 RILRIISALVILLFFTIYCASGIVAGARLFESTFGMSYETALWAGAAATILYTFIGGFLA 182 +LR++SALVIL+FFT Y +SG+VAGA+LFE++FG++YET+LW GA I YTF+GGFLA Sbjct: 121 HMLRVVSALVILIFFTFYTSSGMVAGAKLFEASFGLNYETSLWVGAIVIISYTFLGGFLA 180 Query: 183 VSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIISLM 242 VSWTD +Q LM ALI+ P++ I+ +GG+ + + + + + ++++M++G+ VAIIS + Sbjct: 181 VSWTDFIQGILMFLALIIVPIVAIMELGGWNEVVNTVGEINADHLNMVQGVGAVAIISSL 240 Query: 243 GWGLGYFGQPHILARFMAADSHHSIVHARRISMTWMILCLAGAVAVGFFGIAYFNDHPAL 302 WGLGYFGQPHIL RFMA S + AR I +TWM+L L GA+ GF G+AY D Sbjct: 241 AWGLGYFGQPHILTRFMALRSAKDVPKARFIGITWMVLGLYGAIFTGFVGLAYVADEGNT 300 Query: 303 A-------GAVNQNA--------ERVFIELAQILFNPWIAGILLSAILAAVMSTLSCQLL 347 A V +A E++FI +Q+LFNP +AGILL+AIL+A+MST+ QLL Sbjct: 301 AKLSEFGVQLVTSDAGIQMLGDPEKIFIAFSQVLFNPIVAGILLAAILSAIMSTIDSQLL 360 Query: 348 VCSSAITEDLYKAFLRKHASQKELVWVGRVMVLVVALVAIALAANPENRVLGLVSYAWAG 407 V SSA+ ED YKA LRK+A+ +ELVWVGR+ V V+AL+AI LA NPE+ VL LVSYAWAG Sbjct: 361 VSSSAVAEDFYKAILRKNATDRELVWVGRLSVAVIALIAIILAYNPESSVLNLVSYAWAG 420 Query: 408 FGAAFGPVVLFSVMWSRMTRNGALAGMIIGALTVIVWKQF--GWLGLYEIIPGFIFGSIG 465 FGAAFGP+++ S+ W +TRNGA+AGM++GA+TVI W Q + LYEI+PGF+ + Sbjct: 421 FGAAFGPIIILSLFWKSLTRNGAMAGMVVGAITVIAWDQLVKPFFPLYEIVPGFLLCGLV 480 Query: 466 IVVFSLLGKAPSAAMQKRFAEADA 489 +V SLL K P+ +++ F +A A Sbjct: 481 AIVVSLLDKEPTDEIKQEFEQAKA 504 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: 777 Number of extensions: 50 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: 505 Length adjustment: 34 Effective length of query: 468 Effective length of database: 471 Effective search space: 220428 Effective search space used: 220428 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