Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate WP_020922288.1 RHE_RS18500 TRAP transporter large permease subunit
Query= TCDB::P74224 (445 letters) >NCBI__GCF_000092045.1:WP_020922288.1 Length = 497 Score = 474 bits (1221), Expect = e-138 Identities = 232/440 (52%), Positives = 322/440 (73%), Gaps = 1/440 (0%) Query: 1 MVDYDWLGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFG 60 M D+ + P MF+G ++F+ G+PVAFSL V + F IIG G F FL A+P R FG Sbjct: 1 MFDFGIIPPAMFLGMVIFMLYGFPVAFSLAAVGMFFGIIGIVTGHFSEAFLQALPLRFFG 60 Query: 61 IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTG 120 I++N LLAIPFF +G++LER G+AE LLE G + G + GGLA AVILVG +L A TG Sbjct: 61 IVSNDLLLAIPFFTLMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITG 120 Query: 121 VVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGD 180 VAA+V+ MG+ISLPIMLRYGYS LA+GVI ASGT+ Q+IPPS+VL+VLADQLG SVGD Sbjct: 121 TVAASVITMGVISLPIMLRYGYSPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGD 180 Query: 181 LFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVL 240 +++G++ P ++ F L+VL+++ ++P P LP EVR L +++ M+P +VL Sbjct: 181 MYLGAIGPSILQVTIFVLFVLVMSIVRPKSMPPLPKEVRGDFNWALLVKVLMGMVPSIVL 240 Query: 241 ILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILL 300 I LVLG+IF G+A+PTEAGA+G +GA+ LA N+RL W + E +T ITSMV++IL+ Sbjct: 241 IFLVLGTIFMGLATPTEAGALGVVGAMLLAAMNRRLTWPLIREAMTSTTHITSMVVMILI 300 Query: 301 GSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLF 360 GST FSLVF+G++G R++ +L+ +PGG +GFL I IF+L FF+DFFEIAFIV+P+ Sbjct: 301 GSTCFSLVFQGMDGSRWIEHMLSGIPGGPVGFLIFVNIFIFVLAFFLDFFEIAFIVIPML 360 Query: 361 KPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIG 420 PVA +L +DLIW+GV++ N+QTSF+ PPFGFALFYLR +A + T IY GA+P++G Sbjct: 361 APVASSLGIDLIWFGVLICVNMQTSFMHPPFGFALFYLRSIASKDVKTSDIYMGALPWVG 420 Query: 421 LQVLVLLLIIIFPALIN-WL 439 +Q++++ ++I +P + WL Sbjct: 421 MQIILVAIVIFWPQSVTYWL 440 Lambda K H 0.331 0.148 0.443 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: 754 Number of extensions: 36 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: 445 Length of database: 497 Length adjustment: 33 Effective length of query: 412 Effective length of database: 464 Effective search space: 191168 Effective search space used: 191168 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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