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 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 290 bits (742), Expect = 5e-83 Identities = 165/386 (42%), Positives = 227/386 (58%), Gaps = 9/386 (2%) Query: 24 DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83 D +YR +Q + ++ L+ F W+ N NLA F FL A +EI Q+LI ++ Sbjct: 26 DTRYRGYTFQFIALIALIFFFGWLVSNAIYNLAALGQDINFSFLGQPASYEIDQTLIPYT 85 Query: 84 SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143 S T+ RA VG+LNTLLVA G TATI G L G+ RLS+NWL+AK+ +VYVE+FRNIP Sbjct: 86 STDTHMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIP 145 Query: 144 PLLVIFFWYLGVLSVLPQPRESVG--------LPFSMYLNNRGLAFPKPIFDTGMIAVGI 195 L+ I + LPQPR G L S+ NRG+ P P+++ G V Sbjct: 146 VLIWIVIISAVMSQALPQPRAFRGEDATATMVLWDSVAFTNRGVYIPAPVWNPGSGIVVA 205 Query: 196 ALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAG 255 V++I+ + R+A TG+ ++A+ LL F V G P+ D P G Sbjct: 206 VFVLSIIGIFVFRRYAKNLLFNTGKLLPVGRISLAIFFVPTLLAFFVMGRPIGLDYPELG 265 Query: 256 KFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTR 315 FN GG + ++L+ AL+ YT +FIAE VR GI V KGQ+EAA ALG+ P+ + Sbjct: 266 GFNFRGGINIRGTLIALWFALALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMS 325 Query: 316 LVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLV-AVGGTILNQSGQAIEIVCIWG 374 L+++PQALR+IIPP+ SQYLNLTKNSSLA AIG+ DL +GG LNQ+G++ E V + Sbjct: 326 LIILPQALRVIIPPVISQYLNLTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLM 385 Query: 375 IVYLSLSILTSLFMNWFNAKMALVER 400 + YL +S+ S MN +N + L ER Sbjct: 386 LFYLLISLSISALMNLYNNAVKLKER 411 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: 498 Number of extensions: 20 Number of successful extensions: 3 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: 411 Length adjustment: 31 Effective length of query: 369 Effective length of database: 380 Effective search space: 140220 Effective search space used: 140220 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