Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF3943 Psest_4013 TRAP transporter, DctM subunit
Query= TCDB::P74224 (445 letters) >FitnessBrowser__psRCH2:GFF3943 Length = 458 Score = 438 bits (1126), Expect = e-127 Identities = 221/453 (48%), Positives = 314/453 (69%), Gaps = 20/453 (4%) Query: 5 DWLGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMAN 64 +++ ++F+ L GYPVAF+LGG+A+LFA +G GSFD +L A+P RIFGIM N Sbjct: 3 EFMAILLFISICFALMSGYPVAFTLGGMALLFAGVGVVTGSFDVGYLHALPNRIFGIMNN 62 Query: 65 GTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAA 124 T+LA+P F+F+G MLE+S +AE LLE+M + G +RGGLA++V +VG +LAA+TG+V A Sbjct: 63 QTMLAVPLFVFMGVMLEKSRVAEDLLESMSRLFGTMRGGLAISVCVVGALLAASTGIVGA 122 Query: 125 TVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLG--------- 175 TVV MGL++LP MLR GY +A+G + A+GTLGQIIPPS++L++L D + Sbjct: 123 TVVTMGLLALPTMLRRGYDPAIATGTLAATGTLGQIIPPSIILVLLGDVMSSAFQQAQLK 182 Query: 176 --------VSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELR 227 VSVGDLF+G+L+PGL++ G + LY++ +A +P PALP E +G E Sbjct: 183 MGIFSPKTVSVGDLFVGALIPGLLLVGMYILYLIAVAIFQPKKLPALPQE--ELGPIEWG 240 Query: 228 RRIVQVMLPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDA 287 + ++ +LPPL LI VLGSI G A+PTEA A+G++GA L+ +LN+ L +V Sbjct: 241 K-LIGSLLPPLALITAVLGSILAGYATPTEAAAIGALGATLLSIAKGQLNFTQLKQVAFG 299 Query: 288 TLRITSMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFI 347 T ITSMV LIL+G++ FSLVFRG G+ + D L +LPGG +G + M+ IF+LGF + Sbjct: 300 TTEITSMVFLILIGASLFSLVFRGFGGEVLIEDALHSLPGGVLGAFLVVMLVIFLLGFIL 359 Query: 348 DFFEIAFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLT 407 DF EI F+V+P+ P+ A+ LD +W GV+ NLQTSFLTPPFGF+LFYLRGV P S+ Sbjct: 360 DFIEIIFVVVPIVGPILLAMGLDPVWLGVMFAINLQTSFLTPPFGFSLFYLRGVTPRSVP 419 Query: 408 TGQIYRGAVPFIGLQVLVLLLIIIFPALINWLP 440 T +Y+G +PFI +Q+ +L++ ++P ++ WLP Sbjct: 420 TSVMYKGVLPFIAIQIGMLVVAYMWPGIVTWLP 452 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: 683 Number of extensions: 39 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: 445 Length of database: 458 Length adjustment: 33 Effective length of query: 412 Effective length of database: 425 Effective search space: 175100 Effective search space used: 175100 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