Align Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein (characterized)
to candidate PP_2255 PP_2255 C4-dicarboxylate transport protein
Query= SwissProt::P21345 (437 letters) >FitnessBrowser__Putida:PP_2255 Length = 436 Score = 280 bits (715), Expect = 8e-80 Identities = 158/417 (37%), Positives = 244/417 (58%), Gaps = 16/417 (3%) Query: 7 SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNLLSPAGDIFIHLIKMIVVPIVISTLVV 66 S+ Q++ + LGI G L + S L P GD FI LIKM++ IV +V Sbjct: 8 SIFLQVVLGLALGIACG--LSFPDLSLQ------LKPLGDGFIKLIKMLIGLIVFCVVVS 59 Query: 67 GIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLA--NVFQPGAGVDMSQLATVDISK 124 GI+G GD K++GRIG K++IYFEV+TT+A+++G+ A + GA + + QL+ D + Sbjct: 60 GISGAGDLKKVGRIGLKSVIYFEVLTTLALVIGLVFAFTSGIGSGANIHLDQLSAADANG 119 Query: 125 YQSTTEAVQSSSHGIMGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHREP 184 + + HG + L+PT+++ + A +L ++ FSVLFG L+ L Sbjct: 120 LAERGQHI----HGATAFFMDLIPTSVIGAFADNNILQVLLFSVLFGSALN-LVGDSAAG 174 Query: 185 LVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILFF 244 + + +S +F++ M++R AP+GVF IA T + +G +SL L LV L + F Sbjct: 175 ISRLINELSHVIFRIMGMIVRLAPIGVFGAIAFTTSKYGLASLQHLGGLVALFYLTCAGF 234 Query: 245 ALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSFV 304 L+VLG V RL GL + LI+ L++EL + TASS++VLP+I+ K+E G S V Sbjct: 235 VLIVLGTVMRLSGLKLLPLIKYLREELTIVLGTASSDAVLPQIMRKLEHLGIGSSTVGLV 294 Query: 305 VPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFVV 364 +PTGYSFNLDG ++Y ++A +FIA G L + + ++L +VTSKG G+PG + V+ Sbjct: 295 IPTGYSFNLDGFSIYLTLAIVFIANATGTPLEMTDLLTILLVSLVTSKGAHGIPGSALVI 354 Query: 365 LLATLGSV-GIPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKA 420 L ATL +V IP+ GL + VD + + R N++GN +A + IA+WE D ++A Sbjct: 355 LAATLTAVPAIPVVGLVLVLAVDWFMGIGRALTNLIGNCVATVAIARWEKDIDLERA 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: 492 Number of extensions: 28 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: 436 Length adjustment: 32 Effective length of query: 405 Effective length of database: 404 Effective search space: 163620 Effective search space used: 163620 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