Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate AO356_28885 AO356_28885 sodium:dicarboxylate symporter
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28885 Length = 441 Score = 316 bits (809), Expect = 1e-90 Identities = 173/424 (40%), Positives = 271/424 (63%), Gaps = 18/424 (4%) Query: 1 MKNIKFSLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIV 60 MK +K SL +QI+ A++LG+++G H+ S L P GD FI LIKM++ P+V Sbjct: 5 MKVVK-SLYFQIICAVLLGVVVG---HFWSQQ-----AIALKPLGDAFIKLIKMMIAPVV 55 Query: 61 ISTLVVGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAG--VDMSQLA 118 T+V GIAG+ D + LGR+ +KT++ F +T +++I+G+ +F+PGAG +D +QL+ Sbjct: 56 FCTIVTGIAGMSDKRSLGRLLSKTMLLFLALTVISLIIGLVSVYLFKPGAGMNIDPTQLS 115 Query: 119 TVDISKYQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLP 178 T +S+Y TE+ S ++ + ++P + + KGE+LP++F +VL G LSSL Sbjct: 116 TQGLSQY---TESAAKLS--VVDFFMHIIPDTFIGAFNKGEVLPVLFIAVLCGFALSSL- 169 Query: 179 ATHREPLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVH 238 +P++ V S S +FK+ +MR+AP+G F +A TV +G +SL LAKL++ ++ Sbjct: 170 GERGKPVLEVLESASHMVFKIFSYLMRFAPIGAFGALAFTVGQYGITSLGSLAKLIMTLY 229 Query: 239 FAILFFALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPV 298 A FF VVLG + R G S+W L+R L++E ++ T+S+E V+PR++EK++A G Sbjct: 230 IACAFFVFVVLGSLCRAHGFSLWKLLRYLREEFLVVLGTSSTEPVMPRMLEKLQALGCKK 289 Query: 299 SITSFVVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVP 358 + V+PTGYSFNLDG+ +Y S+AAIFIAQ IDL++ Q I ++ ++++SKG AGV Sbjct: 290 GVVGLVLPTGYSFNLDGTAIYLSLAAIFIAQACNIDLTLTQVITMLAIMLLSSKGAAGVT 349 Query: 359 GVSFVVLLATLGSV-GIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDR 417 G FV L +TL + IPL GLA + G+DR + AR ++ NA+A +VI+ E+ DR Sbjct: 350 GSGFVALASTLTVIHDIPLAGLALLIGIDRFMSEARALTSLASNAVATVVISLSENACDR 409 Query: 418 KKAL 421 + L Sbjct: 410 EVLL 413 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: 465 Number of extensions: 19 Number of successful extensions: 6 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: 441 Length adjustment: 32 Effective length of query: 405 Effective length of database: 409 Effective search space: 165645 Effective search space used: 165645 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