Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate BPHYT_RS16825 BPHYT_RS16825 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__BFirm:BPHYT_RS16825 Length = 441 Score = 309 bits (791), Expect = 1e-88 Identities = 166/409 (40%), Positives = 249/409 (60%), Gaps = 8/409 (1%) Query: 9 QIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 ++ I L+ GI+VGA+F P A L+P+GD FL+LIKM++ PIV +V G+A GDL+ Sbjct: 11 RVVIALVAGIVVGAVF---PHFAQSLRPLGDGFLKLIKMVIGPIVFCVVVSGMAHAGDLR 67 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVN--MKSLEKTDIQSYVDTTNEVQ 126 K+G++G K +IYFE++TTIA+V+G + A + +PG G+N + SL+ + +Y + ++ Sbjct: 68 KVGRVGLKAVIYFEVMTTIALVIGAILAYVTRPGVGMNIDLHSLDPASLSTYTEHAKSLK 127 Query: 127 HHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEAM 186 + I+P + +TGD+L I+ FSV+FG ++ +G K + V ++ Sbjct: 128 --DTAGFLLKIIPDTAINAFATGDILQILVFSVLFGSALSLLGNKAQRVSSLIDELSQVF 185 Query: 187 FYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKLF 246 F V I+K AP GV I T +GVESL L LV+V Y + F+ VLG V +L Sbjct: 186 FRVMGFIIKLAPLGVLGAIAFTTGTYGVESLKQLGMLVLVFYLSCFVFVVVVLGVVMRLA 245 Query: 247 GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDGS 306 G +IF +I+ L++EL + TASS+ VLP+IM K+E G + VIPTGYSFNLDG Sbjct: 246 GFSIFKLIRYLREELSIVLGTASSDAVLPQIMRKLEWMGVKDSTVGLVIPTGYSFNLDGF 305 Query: 307 TLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GIP 365 ++Y LA IFIAQ +SV I ++LV +VTSKG G+PG + V+L ATL + IP Sbjct: 306 SIYLTLAVIFIAQATNTPLSVHDLIVVVLVSLVTSKGAHGIPGSAIVILAATLSAIPAIP 365 Query: 366 VEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYL 414 V GL I +D + +AR N+IGN +A ++++ WE + + + L Sbjct: 366 VLGLVLILPVDWFVGIARALTNLIGNCVATVVVAVWENDIDRARAHRVL 414 Lambda K H 0.326 0.143 0.402 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: 401 Number of extensions: 16 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: 421 Length of database: 441 Length adjustment: 32 Effective length of query: 389 Effective length of database: 409 Effective search space: 159101 Effective search space used: 159101 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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