Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate H281DRAFT_01718 H281DRAFT_01718 aerobic C4-dicarboxylate transport protein
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__Burk376:H281DRAFT_01718 Length = 452 Score = 337 bits (865), Expect = 3e-97 Identities = 181/427 (42%), Positives = 277/427 (64%), Gaps = 18/427 (4%) Query: 11 QILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVVGIAG 70 Q+L ++ GILLG H++ D V + L P GD+FI LI+M++ PI+ +++VVGIA Sbjct: 16 QVLIGIIAGILLG---HFYPD-----VGSQLKPLGDLFIKLIRMLLAPIIFASVVVGIAR 67 Query: 71 VGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAG--VDMSQLATVDISKYQST 128 + D + GR+G K ++YFEV +T+A+++G+ + NVF+PGAG VD S + IS Y T Sbjct: 68 MNDLHEAGRVGVKALLYFEVASTIALLVGMVVVNVFKPGAGMNVDPSHIDGSAISTY--T 125 Query: 129 TEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREPLVTV 188 T A Q HG++ S+VP +IV + A GEMLPIIFFS+L + L+ L P V + Sbjct: 126 TAARQ---HGMLDFFTSIVPNSIVGAFANGEMLPIIFFSLLLAISLARL-GPRTAPFVDM 181 Query: 189 FRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFFALVV 248 + MF V +VM AP+G F +A T+A +G +L +L+L ++ +FF +VV Sbjct: 182 LDMFLQGMFGVVRIVMYVAPIGAFGGMAFTIAKYGIGTLASFGQLMLCLYLTSIFFVVVV 241 Query: 249 LGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFVVPTG 308 LG+V R+CGLS++ +R +KDE+++ TAS+E+VLP+++ KME G + V+PTG Sbjct: 242 LGLVMRMCGLSLFKYLRYIKDEILITLGTASTEAVLPQMLVKMERMGCSRPVVGMVLPTG 301 Query: 309 YSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVVLLAT 368 Y+FN DG+ +Y ++AA+FIAQ + L+IW +++++ L++TSKG AGV G FV L AT Sbjct: 302 YTFNADGTAIYLTMAALFIAQAMNVHLTIWDQLLVLGVLLLTSKGSAGVAGAGFVALAAT 361 Query: 369 LGSV-GIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKALA-YERE 426 L S+ IP+EGL + GVDR L+ AR N++GN +A +V+A+WE + D A A R Sbjct: 362 LASMHKIPVEGLVLLLGVDRFLNEARAVTNLIGNGVATVVVARWEGQLDMNTARAVLNRT 421 Query: 427 VLGKFDK 433 + +F++ Sbjct: 422 YVAEFEE 428 Lambda K H 0.326 0.141 0.403 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: 488 Number of extensions: 25 Number of successful extensions: 5 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: 437 Length of database: 452 Length adjustment: 32 Effective length of query: 405 Effective length of database: 420 Effective search space: 170100 Effective search space used: 170100 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 (21.7 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