Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate AZOBR_RS28110 AZOBR_RS28110 C4-dicarboxylate ABC transporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__azobra:AZOBR_RS28110 Length = 457 Score = 295 bits (756), Expect = 1e-84 Identities = 149/406 (36%), Positives = 251/406 (61%), Gaps = 9/406 (2%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L +Q+ +GL LGI+ G + P + A L+P+GD F++L+KM++ P+V ++V G+ S+ Sbjct: 22 LYFQVVVGLTLGILAGHFW---PDLGASLKPLGDGFVKLVKMMIAPVVFCTIVSGITSLN 78 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMK--SLEKTDIQSYVDTTN 123 D +++GK K++ F +T A+++GL A I +PG G+++ SL+ T Y Sbjct: 79 DTREIGKTLVKSMALFYALTVAALLIGLAAVMIIEPGVGMHVSAASLDPTVAARYAKQAA 138 Query: 124 EVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183 V V ++I+P + F + + G++LP++ SV+ G G+ +G+ G+PV+Q + + Sbjct: 139 PVGFTDFV---LHIIPHSFFGAFAEGEVLPVLLISVLVGFGLTRVGKAGEPVVQGIESFS 195 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243 +F IMK AP G F + TV K+G++S+ L L++ Y F+ V+G +A Sbjct: 196 HVLFAAFGFIMKLAPIGAFGAMAFTVGKYGIDSIGSLGLLILTFYVACGVFLMVVIGTLA 255 Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNL 303 +L G +++ +++ ++EL++ T+SSE VLPR++ K+E GC K ++ V+P GYSFNL Sbjct: 256 RLHGFSLWKVLRYFREELLIVLGTSSSEPVLPRVLQKLEALGCKKGVSGLVLPMGYSFNL 315 Query: 304 DGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV- 362 DG+ +Y LA++FIAQ I +S Q ++L V+++TSKG AGV G FV L+ATL + Sbjct: 316 DGTAIYLTLASLFIAQACDIHLSGGQIFAMLGVMLLTSKGAAGVTGSGFVALVATLTVMP 375 Query: 363 GIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEE 408 +PV G+A + GIDR + AR ++I N +A+I++S WE + E Sbjct: 376 DLPVAGVALLVGIDRFMSEARALTSIISNCVASIVVSIWENACDRE 421 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: 416 Number of extensions: 17 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: 457 Length adjustment: 32 Effective length of query: 389 Effective length of database: 425 Effective search space: 165325 Effective search space used: 165325 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