Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate PP_2056 PP_2056 C4-dicarboxylate transport protein
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__Putida:PP_2056 Length = 435 Score = 307 bits (787), Expect = 4e-88 Identities = 166/415 (40%), Positives = 263/415 (63%), Gaps = 17/415 (4%) Query: 7 SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVV 66 SL +QIL A++LG+++G + + + L P GD FI LIKM++ P+V T+V Sbjct: 6 SLYFQILCAVLLGVVVGHFWAQQAVA--------LKPLGDAFIKLIKMMIAPVVFCTIVT 57 Query: 67 GIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAG--VDMSQLATVDISK 124 GIAG+ D + LGR+ +KT++ F +T V++++G+ +F+PGAG +D + L+T +S+ Sbjct: 58 GIAGMTDKRSLGRLMSKTLLLFLGLTVVSLVIGLAAVYLFKPGAGMNIDPATLSTAGLSQ 117 Query: 125 YQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREP 184 Y T A + S ++ + ++P + + KGE+LP++F +VL G LSS+ +P Sbjct: 118 Y--TASAAKLS---VVDFFMHIIPDTFIGAFNKGEVLPVLFIAVLSGFALSSM-GEKGKP 171 Query: 185 LVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFF 244 ++ V S S +F++ +MR+AP+G F +A TV +G +SL LAKLV ++ A FF Sbjct: 172 VLDVLESASTMVFRIFGYLMRFAPIGAFGALAFTVGQYGITSLGALAKLVGTLYIACAFF 231 Query: 245 ALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFV 304 LVVLG + R G S+W L+R ++E ++ T+S+E VLPR++EK+E G + V Sbjct: 232 VLVVLGGICRAHGFSLWKLLRYFREEFLVVLGTSSTEPVLPRMLEKLEKLGCKKGVVGLV 291 Query: 305 VPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVV 364 +PTGYSFNLDG+ +Y S+AA+FIAQ IDLS+ Q + ++ ++++SKG AGV G FV Sbjct: 292 LPTGYSFNLDGTAIYLSLAAVFIAQACNIDLSLGQVVTMLAIMLLSSKGAAGVTGSGFVA 351 Query: 365 LLATLGSV-GIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRK 418 L +TL + IPL GLA + GVDR + AR ++ NA+A +V++ E+ DR+ Sbjct: 352 LASTLTVIHDIPLAGLALLIGVDRFMSEARALTSLASNAVATVVVSLSENACDRQ 406 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: 482 Number of extensions: 20 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: 435 Length adjustment: 32 Effective length of query: 405 Effective length of database: 403 Effective search space: 163215 Effective search space used: 163215 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