Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate CCNA_00664 CCNA_00664 C4-dicarboxylate transport protein
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__Caulo:CCNA_00664 Length = 417 Score = 321 bits (822), Expect = 3e-92 Identities = 149/405 (36%), Positives = 260/405 (64%), Gaps = 10/405 (2%) Query: 9 QIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVGDLK 68 Q+ I ++LG++VGAI+ P++ L+P+GD F++LIK+++ P++ ++ G+A +GD+K Sbjct: 7 QVLIAIVLGVLVGAIW---PQIGVALKPLGDGFIKLIKLVIAPVIFCTVAGGIARMGDMK 63 Query: 69 KLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMK--SLEKTDIQSYVDTTNEVQ 126 G++G K +IYFE+++T+A+V+GL+ + QPG G N+ +L+ + YV+ + Q Sbjct: 64 AFGRVGVKALIYFEVVSTLALVIGLVVGRLIQPGAGFNIDPATLDASIAAGYVE---KAQ 120 Query: 127 H-HSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTAEA 185 H MV ++++P + G++L ++ +++ G +G+ G+ V T++ Sbjct: 121 HGEGMVAYLLHLIPDTFIGAFADGNLLQVLVIAILTGFACVRMGDFGEKVAHVLDETSKL 180 Query: 186 MFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVAKL 245 F + + +++ AP G F +G T+ K+GVE+L+ L LV Y T + F+ VVLGG+A + Sbjct: 181 FFGIIHIVVRLAPIGAFGAMGFTIGKYGVEALVQLGALVATFYVTSLLFVLVVLGGIAWV 240 Query: 246 FGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNLDG 305 G +IF + +++EL++ T+SSE+VLP++MEK+EN G +++ VIPTGYSFNLDG Sbjct: 241 SGFSIFRFLAYIREELLIVLGTSSSESVLPQMMEKLENAGARRSVVGLVIPTGYSFNLDG 300 Query: 306 STLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV-GI 364 + +Y LA +F+AQ + + Q+++LL V M+TSKG +GV G F+ L ATL V I Sbjct: 301 TNIYMTLATLFLAQATNTPLSLGQELALLGVAMLTSKGASGVTGAGFITLAATLAVVPDI 360 Query: 365 PIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEK 409 PI LA + G+DR + R N++GN +A +++++WEG + ++ Sbjct: 361 PIAALAILVGVDRFMSECRALTNLVGNGVATLVVARWEGALDRQR 405 Lambda K H 0.326 0.143 0.404 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: 429 Number of extensions: 18 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: 417 Length adjustment: 32 Effective length of query: 389 Effective length of database: 385 Effective search space: 149765 Effective search space used: 149765 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: 50 (23.9 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