Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate Ac3H11_719 Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_719 Length = 456 Score = 310 bits (794), Expect = 6e-89 Identities = 167/415 (40%), Positives = 260/415 (62%), Gaps = 17/415 (4%) Query: 8 LAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVVG 67 L +Q++ A+VLG+LLG + + ++ L P GD FI L+KMI+ P++ T+V G Sbjct: 20 LYFQVVLAIVLGVLLGHFEPSYGEA--------LKPLGDAFIKLVKMIIAPVIFLTIVTG 71 Query: 68 IAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVDISKYQS 127 IAG+ +GR+ K + YF +T+A+++G+ +ANV QPGAG++++ +A +D QS Sbjct: 72 IAGMSQLSTVGRVFGKAMAYFLFFSTLALVVGLVVANVVQPGAGMNIN-VADLD----QS 126 Query: 128 TTEAVQSSSHG--IMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREPL 185 + + SH + G L ++P +V+ +L ++ +VLFG+GL+ + R P+ Sbjct: 127 AVKGYVAKSHEMTLTGFALDIIPKTLVSPFVGDNILQVLLVAVLFGVGLAMVGDAGR-PV 185 Query: 186 VTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFFA 245 + +++ +FKV +VM+ AP+G F +A T+ FG SL LA LV + L F Sbjct: 186 LNFLDALTTPVFKVVGIVMKAAPLGAFGAMAFTIGKFGLGSLVNLAWLVGSFYITSLLFV 245 Query: 246 LVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFVV 305 +V+LG VARLCG SV+ L R LK EL+L T+SSES LP ++EKME G S+ VV Sbjct: 246 VVILGFVARLCGFSVFKLCRYLKAELMLVLGTSSSESALPSLMEKMEKAGCSKSVVGLVV 305 Query: 306 PTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVVL 365 PTGYSFNLDG+ +Y ++AA+FIAQ +L++ ++ L+L M++SKG AGV G F+ L Sbjct: 306 PTGYSFNLDGTNIYMTLAALFIAQATNTELTLGHQVALLLVAMLSSKGAAGVTGAGFITL 365 Query: 366 LATLGSV-GIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKK 419 ATL V +P+ G+A I GVDR + R+ N +GNA+A +V+++WE+ D ++ Sbjct: 366 AATLAVVPEVPVAGMALILGVDRFMSECRSLTNFIGNAVATVVVSRWENALDHER 420 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: 515 Number of extensions: 26 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: 456 Length adjustment: 33 Effective length of query: 404 Effective length of database: 423 Effective search space: 170892 Effective search space used: 170892 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