Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate PfGW456L13_2016 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2016 Length = 444 Score = 321 bits (823), Expect = 3e-92 Identities = 169/411 (41%), Positives = 266/411 (64%), Gaps = 13/411 (3%) Query: 7 SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVV 66 SL +Q++ A+ +GILLG H++ + L P GD FI LIKM++ PI+ T+V Sbjct: 10 SLYFQVIVAIAIGILLG---HFYPQTGV-----ALKPLGDGFIKLIKMVIAPIIFCTVVS 61 Query: 67 GIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVDISKYQ 126 GIAG+ + K +G+ G ++YFE+++T+A+++G+ + NV QPGAG+ + ++T+D SK Sbjct: 62 GIAGMQNMKSVGKTGGYALLYFEIVSTLALLIGLVVVNVVQPGAGMHID-VSTLDTSKIA 120 Query: 127 STTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREPLV 186 A + S I+ +L+++P IV + A G++L ++ FSV+FG L L A + +P++ Sbjct: 121 GFISAGKDQS--IIAFVLNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGA-YGKPVL 177 Query: 187 TVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFFAL 246 + MF + +M+M+ APVG F +A T+ +G SL L +L++ + + F L Sbjct: 178 DFIDRFAHVMFNIINMIMKLAPVGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCILFVL 237 Query: 247 VVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFVVP 306 +VLG + R G SV LIR +++EL++ T+SSES LPR++ K+E GA S+ V+P Sbjct: 238 LVLGAICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKLERLGAQKSVVGLVIP 297 Query: 307 TGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVVLL 366 TGYSFNLDG+++Y ++AA+FIAQ + + +I L+L L+++SKG AGV G F+VL Sbjct: 298 TGYSFNLDGTSIYLTMAAVFIAQATDTPMDLTAQITLLLVLLLSSKGAAGVTGSGFIVLA 357 Query: 367 ATLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFD 416 ATL +VG +P+ GLA I G+DR + AR N+VGNA+A LV+AKW + D Sbjct: 358 ATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATLVVAKWVKELD 408 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: 24 Number of successful extensions: 4 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: 444 Length adjustment: 32 Effective length of query: 405 Effective length of database: 412 Effective search space: 166860 Effective search space used: 166860 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