Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF3978 HP15_3918 trap-type mannitol/chloroaromatic compound transport system, large permease component
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Marino:GFF3978 Length = 436 Score = 330 bits (847), Expect = 4e-95 Identities = 170/434 (39%), Positives = 269/434 (61%), Gaps = 8/434 (1%) Query: 10 MMFVGALVF-LGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGTLL 68 ++F G+L+F L G P+AF LGGV+++F FD ++ A +I+G M + TL+ Sbjct: 8 LLFFGSLLFFLLLGLPLAFVLGGVSVVFLYF---TWGFDSFYMVA--SQIWGTMGSFTLV 62 Query: 69 AIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVA 128 AIP F+F+ +LER+G+A L M + G LRGGLAL + + + AA G+ A VVA Sbjct: 63 AIPLFVFMAMILERTGVARDLYRMMHLWCGGLRGGLALGTLGICAVFAAMVGISGAAVVA 122 Query: 129 MGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSLLP 188 MG I+LP ML GY K +A GVI G G +IPPS+++I+ A GVSVG +F ++P Sbjct: 123 MGTIALPSMLERGYDKSMALGVINTGGGWGILIPPSILMILYALITGVSVGKMFAAGIMP 182 Query: 189 GLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVLGSI 248 G+++ A+Y+++ L+P+LAPALP E R ++ R ++ +L P+ ++++VLGSI Sbjct: 183 GVLLMVLTAIYIIVRCHLQPELAPALPKEDRGTWPEKFRA--LRAVLLPIGVVVMVLGSI 240 Query: 249 FFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLILLGSTAFSLV 308 GI +PTEA A+G +GA+ A ++ W L E T ++T M+M IL + AFS Sbjct: 241 IGGITTPTEAAAMGVLGALISAAVYRQFKWSILKEAAIRTFKLTGMIMWILFAAHAFSAA 300 Query: 309 FRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEALN 368 ++ + + L+ +PGG G + M+ +F+L +D I I LP+F P+ E+L Sbjct: 301 YQSMGAQELIEGLMNMVPGGPWGIIIAMMVIVFLLAMVLDPVGIMLITLPVFMPIVESLG 360 Query: 369 LDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVLLL 428 D IW+G++ N++ ++TPPFGF LFYL+G+ P S+T IY+ +PF+ ++++ ++L Sbjct: 361 FDPIWFGILFVINMEIGYMTPPFGFNLFYLKGIVPPSITMKDIYKSIIPFVIVEIVGIIL 420 Query: 429 IIIFPALINWLPSL 442 I++FP + WLP L Sbjct: 421 IMVFPEIATWLPDL 434 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: 580 Number of extensions: 36 Number of successful extensions: 3 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: 436 Length adjustment: 32 Effective length of query: 413 Effective length of database: 404 Effective search space: 166852 Effective search space used: 166852 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 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