Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate RR42_RS26105 RR42_RS26105 C4-dicarboxylate transporter
Query= CharProtDB::CH_088342 (421 letters) >FitnessBrowser__Cup4G11:RR42_RS26105 Length = 462 Score = 357 bits (915), Expect = e-103 Identities = 172/399 (43%), Positives = 268/399 (67%), Gaps = 5/399 (1%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L +Q+ +++G+I+G + P+ A ++P+GD F++LIKMI+ PI+ ++VVG+A + Sbjct: 26 LYFQVITAIVIGVILGHFY---PQAGAAMKPLGDGFIKLIKMIIAPIIFCTVVVGIAGME 82 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKTDIQSYVDTTNEV 125 D+KK+GK GG ++YFE+++ IA+VVGL+ NI +PG G+N+ + D +S T Sbjct: 83 DMKKVGKTGGLALLYFEVVSAIALVVGLVIINIAKPGVGMNV-DVSTLDTKSIAAYTGPG 141 Query: 126 QHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEA 185 + V+ ++++P + ++ + G++L ++ F+VMFG + G +G V F + + Sbjct: 142 KMQGTVDFLLHVIPNTVVDAFAQGEILQVLLFAVMFGFALHKFGGRGTLVFDFIEKFSHV 201 Query: 186 MFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVAKL 245 +F + IMK AP G F + T+ K+GV SL+ L +L+ YAT LFFIF VLGG+A+ Sbjct: 202 LFAIVGYIMKVAPIGAFGAMAFTIGKYGVGSLLQLGQLMATFYATCLFFIFVVLGGIARA 261 Query: 246 FGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNLDG 305 G +I+ IK +K+EL++ T+SSE+VLPR+M K+E G K++ VIPTGYSFNLDG Sbjct: 262 HGFSIWKFIKYIKEELLIVLGTSSSESVLPRMMAKLENLGARKSVVGLVIPTGYSFNLDG 321 Query: 306 STLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG-I 364 +++Y +AA+FIAQ +MS++QQ++LL VL++TSKG AGV G F+VL ATL VG + Sbjct: 322 TSIYLTMAAVFIAQATNTEMSLTQQLTLLAVLLLTSKGAAGVTGSGFIVLAATLSAVGHV 381 Query: 365 PVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEG 403 PV GLA I GIDR + AR N+IGN +A ++++KW G Sbjct: 382 PVAGLALILGIDRFMSEARALTNLIGNGVATVVVAKWTG 420 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: 426 Number of extensions: 19 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: 462 Length adjustment: 32 Effective length of query: 389 Effective length of database: 430 Effective search space: 167270 Effective search space used: 167270 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