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 WP_012384590.1 BIND_RS08115 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000019845.1:WP_012384590.1 Length = 391 Score = 313 bits (801), Expect = 7e-90 Identities = 177/381 (46%), Positives = 233/381 (61%), Gaps = 13/381 (3%) Query: 24 DPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFS 83 DP+ R Q L ++ L + + N+ + F F AGF+I Q+ I +S Sbjct: 20 DPRKRGFIVQALFVLALCLVLVGMFTTLHANMVARGIPTDFSFWNQTAGFDINQTPIAYS 79 Query: 84 SDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIP 143 STY RA LVG++NTL+VA G+ TIIG ++GI RLS+N L++ L YVE RNIP Sbjct: 80 PLSTYGRAFLVGLINTLIVASIGLVCTTIIGVIVGISRLSKNRLVSFLAATYVETLRNIP 139 Query: 144 PLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVA 203 LL + FWY +L LP PR+S+ PF LNNRGL P P G VG AL + + A Sbjct: 140 LLLQLLFWYNAILKPLPGPRQSLLFPFGTVLNNRGLFLPLPSLLPGAAWVGAALALGLAA 199 Query: 204 SIIIARWAHKRQAATGQPFHTVW--TAIALIVGL-PLLVFVVSGFPLTFDVPVAGKFNLT 260 S ++ R G W T + L++ L P ++ + PL FD P+ FN T Sbjct: 200 SFLVGR---------GTALKPGWPKTLLCLVLALGPAIIAAMLAPPLAFDRPILKGFNYT 250 Query: 261 GGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVP 320 GG V PE ++L L LS YTA+FIAEI+R GI VP+GQSEAA ALGL R +++P Sbjct: 251 GGFRVLPELVALLLGLSLYTAAFIAEIIRAGIMAVPRGQSEAAEALGLPSGLTMRRIILP 310 Query: 321 QALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAV-GGTILNQSGQAIEIVCIWGIVYLS 379 QALR++IPPLTSQYLNL KNSSLA+ IG+ DLV V GT+LNQ+G A++I+ I VYL+ Sbjct: 311 QALRVVIPPLTSQYLNLIKNSSLAVFIGYPDLVQVFAGTVLNQTGAAVQIIFITMAVYLA 370 Query: 380 LSILTSLFMNWFNAKMALVER 400 +S++TS MN N +MALVER Sbjct: 371 VSLVTSFAMNLINRRMALVER 391 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: 492 Number of extensions: 29 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: 391 Length adjustment: 31 Effective length of query: 369 Effective length of database: 360 Effective search space: 132840 Effective search space used: 132840 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 24 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