Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate WP_057508017.1 ABB28_RS07385 dicarboxylate/amino acid:cation symporter
Query= SwissProt::P24943 (421 letters) >NCBI__GCF_001431535.1:WP_057508017.1 Length = 447 Score = 343 bits (881), Expect = 5e-99 Identities = 165/409 (40%), Positives = 270/409 (66%), Gaps = 9/409 (2%) Query: 6 LAWQIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65 L +Q+ + +ILG ++G + P V ++P+GD F+ L+KMI+ P++ ++V G+A + Sbjct: 20 LYFQVVVAIILGAVLG---HYEPLVGEKMKPLGDAFINLVKMIIAPVIFLTIVTGIAGMT 76 Query: 66 DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMK--SLEKTDIQSYVDTTN 123 L+ +G++ K + YF +T+A+VVG++ A++ QPG G+N+ L++T + SYV+ ++ Sbjct: 77 HLRTVGRVFAKAMAYFMFFSTLALVVGMIVAHVVQPGAGMNINPADLDQTAVNSYVEKSH 136 Query: 124 EVQHHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183 ++ +++ ++I+PK + + G++L ++F +V+FG+ +A +GEKGKPVL F + Sbjct: 137 DL---TLIGFAMDIIPKTLVSAFVDGNILQVLFVAVLFGIALALVGEKGKPVLNFLEALV 193 Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVA 243 +F + + +MK AP G F I T+ K+GV SLI L+ LV Y T F+ V+LG VA Sbjct: 194 APVFKLVHILMKAAPIGAFGAIAFTIGKYGVGSLINLAWLVGSFYLTAFLFVVVILGAVA 253 Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNL 303 +L G ++F + + LK EL+L T+SSE+ LP +MEKME GC K++ V+PTGYSFNL Sbjct: 254 RLCGFSVFKLARYLKAELLLVLGTSSSESALPSLMEKMERAGCSKSVVGLVVPTGYSFNL 313 Query: 304 DGSTLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV- 362 DG+ +Y LAA+FIAQ ++ + QI+LLLV M++SKG AGV G F+ L ATL V Sbjct: 314 DGTNIYMTLAALFIAQATNTELTLGHQIALLLVAMLSSKGAAGVTGAGFITLAATLAVVP 373 Query: 363 GIPIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGK 411 +P+ G+A I G+DR + R+ N IGN++A +++S+WEG + ++ K Sbjct: 374 EVPVAGMALILGVDRFMSECRSLTNFIGNAVATVVVSRWEGALDRDRLK 422 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: 416 Number of extensions: 21 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: 447 Length adjustment: 32 Effective length of query: 389 Effective length of database: 415 Effective search space: 161435 Effective search space used: 161435 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 24 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