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 GFF2245 HP15_2195 amino acid ABC transporter, permease protein
Query= TCDB::Q52813 (400 letters) >FitnessBrowser__Marino:GFF2245 Length = 395 Score = 380 bits (977), Expect = e-110 Identities = 202/401 (50%), Positives = 268/401 (66%), Gaps = 7/401 (1%) Query: 1 MTHEAVDTTPLHGTGWSFRSAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNT 60 M + +DT P W YDP+ RS+F+Q + I ++ W + NT N+ Sbjct: 1 MKKQTIDTRPAGPKPW------YDPRVRSLFFQAVAIALVFWGGWILVDNTLSNMESRGI 54 Query: 61 ASGFGFLRGRAGFEIGQSLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIG 120 ++GFGFL AGF I +L+ + + +Y R VG+ NTLLV+ G+ ATI+GF+IG+ Sbjct: 55 STGFGFLGETAGFGIIMNLVPYDATMSYGRTFWVGLTNTLLVSAMGVVAATILGFIIGVA 114 Query: 121 RLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLA 180 RLS NWL+AK+ VY+EV RNIP LL IFFWY VLS LP PR+SV + +++LNNRGL Sbjct: 115 RLSSNWLVAKMALVYIEVIRNIPLLLQIFFWYFAVLSNLPSPRQSVDVGGALFLNNRGLY 174 Query: 181 FPKPIFDTGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVF 240 P P+ G V +++AI A + I WA KRQ ATGQ F T +A++V +P++ + Sbjct: 175 LPDPVTQEGFGIVWGGILLAIAAVVGIRIWAKKRQLATGQIFPTFKVGVAILVLVPIISY 234 Query: 241 VVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQS 300 +V+G PL +D+P FN GG + PE +L++ALS YTASFIAEIVR GI V KGQ+ Sbjct: 235 LVAGRPLEWDLPALRGFNFGGGITIIPELAALWIALSLYTASFIAEIVRSGILSVSKGQT 294 Query: 301 EAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTI 359 EA+ ALGL RLVV+PQA+R+IIPPLTSQYLNL KNSSLA AIG+ DLVAV GT Sbjct: 295 EASKALGLPNGLTLRLVVIPQAMRVIIPPLTSQYLNLVKNSSLATAIGYPDLVAVFMGTT 354 Query: 360 LNQSGQAIEIVCIWGIVYLSLSILTSLFMNWFNAKMALVER 400 LNQ+GQA+E+V I VYL++S+L SLFMN +N +A+ ER Sbjct: 355 LNQTGQAVEVVAITMAVYLTISLLISLFMNIYNRAVAIKER 395 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: 576 Number of extensions: 27 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: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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