Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF1039 Psest_1072 TRAP transporter, DctM subunit
Query= TCDB::P74224 (445 letters) >FitnessBrowser__psRCH2:GFF1039 Length = 456 Score = 372 bits (956), Expect = e-107 Identities = 197/442 (44%), Positives = 289/442 (65%), Gaps = 13/442 (2%) Query: 11 MFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGS-FDPIF-------LSAMPQRIFGIM 62 MF + L G+PVA+SL G+ +LFA++G L FD + + RI+GI+ Sbjct: 11 MFASFMGLLLLGFPVAWSLAGIGLLFAVLGYVLVEHFDANLWFTWDGTIGVLDARIYGIV 70 Query: 63 ANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVV 122 AN ++A+P FIF+G ML+RSGIAE+L+ ++ +LG LRGG A+ V++VG +LAA+TG+V Sbjct: 71 ANELMVALPLFIFMGIMLDRSGIAERLMHSLVRVLGPLRGGYAVTVVVVGILLAASTGIV 130 Query: 123 AATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVS---VG 179 A+V +G++S+ ML+ Y+K LA G + GTLG +IPPS++L+++AD+LG S VG Sbjct: 131 GASVALLGMLSIGPMLQANYNKSLAVGTACSVGTLGILIPPSIMLVLMADRLGTSEASVG 190 Query: 180 DLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLV 239 LF+G+L+PG+M+A + LY++I+AWLK D APA P + + L + ++PPL Sbjct: 191 KLFMGALIPGMMLALMYILYIVIVAWLKKDFAPA-PVNRPKLDARALLD-VFWAVVPPLA 248 Query: 240 LILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQRLNWKALWEVCDATLRITSMVMLIL 299 LI VLGSIFFGIA+ TEA AVG+ GA+ +A ++RLN L + T R + + I Sbjct: 249 LIFAVLGSIFFGIATTTEASAVGAFGALLMAAASRRLNLPVLKDALYQTSRTAAFIFGIF 308 Query: 300 LGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPL 359 +G+T F+ V RGL GD + L LP GQ G L + F+LGFF+D+ EI I+LPL Sbjct: 309 IGATVFAAVLRGLGGDDVIRAALTGLPFGQTGVLLTVLAITFLLGFFLDWVEITLIILPL 368 Query: 360 FKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFI 419 PV ++ +D +W+ ++ LQTSFLTPP GFALFY++GV P +TT +Y G +P+I Sbjct: 369 VAPVLFSMGVDPLWFAILFALCLQTSFLTPPVGFALFYIKGVCPPGITTRDVYLGVLPYI 428 Query: 420 GLQVLVLLLIIIFPALINWLPS 441 +Q++ L L+ F L WLP+ Sbjct: 429 VIQLIGLALVFYFAPLATWLPN 450 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: 618 Number of extensions: 29 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: 456 Length adjustment: 33 Effective length of query: 412 Effective length of database: 423 Effective search space: 174276 Effective search space used: 174276 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