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 Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__SynE:Synpcc7942_0247 Length = 377 Score = 228 bits (580), Expect = 3e-64 Identities = 137/369 (37%), Positives = 207/369 (56%), Gaps = 15/369 (4%) Query: 27 YRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFSSDS 86 +R ++ ++ +V+ +G +W V N NL++ + F +L AGF IG+S I + + Sbjct: 18 WRWVWQLLVLLVVGLGAIWLV-DNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTAD 76 Query: 87 TYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLL 146 +YARAL+VG++N+L V G+ T+IG L G+ S NWL+ +L YV V RN P LL Sbjct: 77 SYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLL 136 Query: 147 VIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASII 206 + WY +L LP ++ S+YL+ +G+ P P G +VI +A ++ Sbjct: 137 QLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQ------TPGWLVVILAIALVL 190 Query: 207 IARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVG 266 W +RQ + + + ++ AIA++ L LL + +P + GG + Sbjct: 191 FVSWLAQRQRSP-RDWRWLYGAIAVVTVLMLLTQL--SWPQQLQPG-----QIRGGLRLS 242 Query: 267 PEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRII 326 EF +L L L YT +FI EI+RGGI VP GQ EAA ALGL S +VVPQALR+I Sbjct: 243 LEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVI 302 Query: 327 IPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSL 386 +P L SQY+ KNSSLAIA+G+ DL A T LNQ+G+ +E+ I + YL+++ + S Sbjct: 303 VPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISA 362 Query: 387 FMNWFNAKM 395 MN ++ Sbjct: 363 GMNGLQQRL 371 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: 483 Number of extensions: 22 Number of successful extensions: 2 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: 377 Length adjustment: 30 Effective length of query: 370 Effective length of database: 347 Effective search space: 128390 Effective search space used: 128390 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