Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate PP_1188 PP_1188 C4-dicarboxylate transport protein
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__Putida:PP_1188 Length = 440 Score = 325 bits (832), Expect = 2e-93 Identities = 172/416 (41%), Positives = 262/416 (62%), Gaps = 17/416 (4%) Query: 7 SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVV 66 SL Q+L A+ +GILLG HY+ ++ L P GD F+ LIKM++ PI+ T+V Sbjct: 10 SLYVQVLVAITIGILLG---HYYPETGV-----ALKPLGDGFVKLIKMVIAPIIFCTVVS 61 Query: 67 GIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAG--VDMSQLATVDISK 124 GIAG+ K +G+ G ++YFE+++T+A+I+G+ + NV +PGAG +D+S L ++ Sbjct: 62 GIAGMQSMKSVGKTGGYALLYFEIVSTIALIIGLVVVNVVKPGAGMHIDVSTLNASSVAA 121 Query: 125 YQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREP 184 Y A + +G +L+++P +V + A G++L ++ FSVLFG L L ++ +P Sbjct: 122 Y-----AAAGAQQTTVGFLLNVIPNTVVGAFANGDILQVLMFSVLFGFALHRL-GSYGKP 175 Query: 185 LVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFF 244 ++ + + MF + +M+M+ AP+G F +A T+ +G SL L L+ + L F Sbjct: 176 VLDMIDRFAHVMFNIINMIMKLAPIGAFGAMAFTIGQYGVGSLVQLGYLMACFYITCLLF 235 Query: 245 ALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFV 304 LVVLG + R G SV LIR +++EL++ T+SSES LPR++ KME GA S+ V Sbjct: 236 VLVVLGGICRAHGFSVIKLIRYIREELLIVLGTSSSESALPRMLAKMERLGAKKSVVGLV 295 Query: 305 VPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVV 364 +PTGYSFNLDG+++Y ++AA+FIAQ + I +I L+L L+V SKG AGV G F+V Sbjct: 296 IPTGYSFNLDGTSIYLTMAAVFIAQATDTTMDITHQITLLLVLLVASKGAAGVTGSGFIV 355 Query: 365 LLATLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKK 419 L ATL +VG +P+ GLA I G+DR + AR N+VGNA+A +V+AKW + D K Sbjct: 356 LAATLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKEMDNDK 411 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: 483 Number of extensions: 21 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: 440 Length adjustment: 32 Effective length of query: 405 Effective length of database: 408 Effective search space: 165240 Effective search space used: 165240 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