Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate GFF195 PGA1_c01990 glutamate/glutamine/aspartate/asparagine transport system permease protein BztB
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Phaeo:GFF195 Length = 410 Score = 301 bits (772), Expect = 2e-86 Identities = 173/394 (43%), Positives = 251/394 (63%), Gaps = 20/394 (5%) Query: 24 DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83 D +YRS+ +Q + ++L +W++ +N NL + +GFL +G++I Q LI + Sbjct: 20 DTRYRSLTFQAIAALVLALAIWYLGNNLIQNLRAAGLNISYGFLGDPSGYDINQRLIEYD 79 Query: 84 SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143 S S++ARA +VG+LNTLLVAV TATI G + G+ RLS NWL++KL VYVE+FRNIP Sbjct: 80 SQSSHARAAVVGVLNTLLVAVLACITATIFGVVAGVLRLSNNWLVSKLMAVYVEIFRNIP 139 Query: 144 PLLVIFFWYLGVLSVLPQPRESVG------LPFSMY-LNNRGLAFPKPIFDTGMIAVG-- 194 L+ I + + +V+P PRE G + F ++ NRG+ P P F++G A G Sbjct: 140 VLIWIIIIFTIMTAVMPGPREFRGDNATSSMLFDLFAFTNRGVYIPMPWFESGFFASGAL 199 Query: 195 --IALVIAIVASIIIARW----AHKRQAATGQPFHTVWTAIAL-IVGLPLLVFVVSGFPL 247 + ++ A+V S ++ R A K Q TG T A+ + +V L L++FV+ L Sbjct: 200 NWLVVIAALVGSFLVMRRIEANATKTQEKTGVRPKTKLIALGVWLVPLALVLFVMG---L 256 Query: 248 TFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALG 307 +++VP FN GG +G ++L+ ALS YT +FIAE VR GI+ + KGQ+EAA ALG Sbjct: 257 SWEVPELKGFNFKGGIKIGGPLIALWFALSIYTGAFIAENVRAGIQAINKGQTEAAAALG 316 Query: 308 LHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVA-VGGTILNQSGQA 366 L P + LVV+PQALR+IIPPL S +LN+TKNSSLAIA+G++D+ A +GG LNQ+G+A Sbjct: 317 LRPGRIMNLVVLPQALRVIIPPLISNFLNITKNSSLAIAVGYADITATLGGITLNQTGRA 376 Query: 367 IEIVCIWGIVYLSLSILTSLFMNWFNAKMALVER 400 IE V + + YL+ S+L S+ MN +NA + L ER Sbjct: 377 IECVLLLMLFYLTASLLISMVMNVYNASVKLKER 410 Lambda K H 0.327 0.141 0.432 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: 481 Number of extensions: 23 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: 400 Length of database: 410 Length adjustment: 31 Effective length of query: 369 Effective length of database: 379 Effective search space: 139851 Effective search space used: 139851 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: 50 (23.9 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