Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate AZOBR_RS21140 AZOBR_RS21140 C4-dicarboxylate ABC transporter
Query= SwissProt::P24943 (421 letters) >FitnessBrowser__azobra:AZOBR_RS21140 Length = 433 Score = 389 bits (999), Expect = e-113 Identities = 188/417 (45%), Positives = 292/417 (70%), Gaps = 12/417 (2%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L Q+ + +GI++G + P +A ++P+GD+F+++IKM++ PIV ++V G++S+G Sbjct: 16 LTVQVLTAITIGILLGHFY---PALAVQMKPLGDVFIKMIKMVIGPIVFLTVVTGISSIG 72 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMK--SLEKTDIQSYVDTTN 123 D+KK+GK+GGK I+YFEI+TT A+ +GLL N+ +PG+G+N++ SL+ + Y Sbjct: 73 DMKKVGKVGGKAILYFEIVTTFALGLGLLVVNLVKPGSGMNIQAGSLKADAVAKYA---T 129 Query: 124 EVQHHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183 E Q+H+ ++ VNIVP N+ + KGDML I+FF+V+FG+ ++A+G+KGK V F+ + Sbjct: 130 EAQNHTTIDFLVNIVPDNVIGAFVKGDMLQILFFAVIFGVALSAMGQKGKVVEDMFEKVS 189 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVA 243 A+F V +M+ AP G F + T+ K+GV SL L +L+ VY TM F+FVVLG +A Sbjct: 190 HALFGVIGILMRVAPLGAFGAMSFTIGKYGVSSLTSLGQLMAAVYITMALFVFVVLGSIA 249 Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNL 303 +L+ ++ ++ +KDEL++ T+SSE+VLP++MEKM+ FGC K + VIPTGYSFNL Sbjct: 250 RLYNFSLLTFLRYIKDELLIVLGTSSSESVLPRMMEKMQKFGCSKHVVGLVIPTGYSFNL 309 Query: 304 DGSTLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363 DG+++Y ++AAIFIAQ + ID+ I QQ+++L +LM+TSKG A V G FV L ATL G Sbjct: 310 DGTSIYLSMAAIFIAQAFNIDLTIWQQLTILGLLMLTSKGAAAVTGGGFVTLAATLSATG 369 Query: 364 -IPIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYIAQLQQ 419 +PIEGLA + G+DR + AR N+IGN +A I+++K EG+++E K +A+ Q+ Sbjct: 370 HLPIEGLALLLGVDRFMSEARAITNLIGNGVATIVVAKMEGEFDESKA---VAEYQE 423 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: 465 Number of extensions: 20 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: 433 Length adjustment: 32 Effective length of query: 389 Effective length of database: 401 Effective search space: 155989 Effective search space used: 155989 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