Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate WP_034212615.1 N787_RS08375 TRAP transporter large permease subunit
Query= TCDB::P74224 (445 letters) >NCBI__GCF_000747155.1:WP_034212615.1 Length = 460 Score = 456 bits (1174), Expect = e-133 Identities = 244/448 (54%), Positives = 307/448 (68%), Gaps = 22/448 (4%) Query: 10 MMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGTLLA 69 ++ +G L G+PVAF LGGVA+L A G GSFDP FL A P R+FG+M N TL+A Sbjct: 13 LLLLGLFAGLASGFPVAFVLGGVALLAAGAGMLTGSFDPSFLEAFPNRVFGVMTNETLVA 72 Query: 70 IPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVAM 129 +P F+F+G MLE+S IAE LLE + + G +RGGL +AV+LVG +LAA+TG+V ATVVAM Sbjct: 73 VPLFVFMGVMLEKSRIAESLLEAVASLFGQVRGGLVVAVLLVGALLAASTGIVGATVVAM 132 Query: 130 GLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLG-------------- 175 GLISLP MLR GY LASG I ASGTLGQIIPPS+VL++L DQLG Sbjct: 133 GLISLPTMLRNGYCPRLASGAICASGTLGQIIPPSIVLVLLGDQLGNAYQQAQLKQGIFA 192 Query: 176 ---VSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQ 232 +SVGDLF G+L+PGL + G + Y L +AW +P APA+ A + G L + IV Sbjct: 193 PETISVGDLFAGALVPGLGLVGLYLAYALWVAWRQPVRAPAV-ASLAPRGKLALAKAIV- 250 Query: 233 VMLPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRIT 292 P L LILLVLGSI G A+ TEA AVG++GA A + +L W L EV + T+R+T Sbjct: 251 ---PALSLILLVLGSILGGFATATEAAAVGAVGATVFAAMHGQLGWARLREVSEQTVRVT 307 Query: 293 SMVMLILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEI 352 +MV ILLG+ FSLVFRG GD + + L LPGG+ G + M+ +F+LGF +DF EI Sbjct: 308 AMVFAILLGAALFSLVFRGYGGDELVHEALTALPGGKWGAVVAVMLLMFLLGFVLDFIEI 367 Query: 353 AFIVLPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIY 412 F+V+P+ PV AL +D +W GV++ NLQTSFLTPPFGFALFYLRGVAP L TG IY Sbjct: 368 VFVVVPIVGPVLLALGVDPVWLGVMMAINLQTSFLTPPFGFALFYLRGVAPPELATGDIY 427 Query: 413 RGAVPFIGLQVLVLLLIIIFPALINWLP 440 RG VPFIGLQ+L+L L+ +FP+L LP Sbjct: 428 RGVVPFIGLQLLMLALVALFPSLATALP 455 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: 674 Number of extensions: 40 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: 460 Length adjustment: 33 Effective length of query: 412 Effective length of database: 427 Effective search space: 175924 Effective search space used: 175924 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 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