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 YP_004143815.1 Mesci_4656 polar amino acid ABC transporter inner membrane subunit
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000185905.1:YP_004143815.1 Length = 395 Score = 514 bits (1323), Expect = e-150 Identities = 253/381 (66%), Positives = 305/381 (80%) Query: 20 SAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSL 79 S + DPK R IF+Q+L +V+LV VWW+AHN NL R ASGFGFL+GRAGF+I +S Sbjct: 15 SFINDPKIRGIFFQVLVVVLLVAGVWWIAHNVIDNLTRLRIASGFGFLKGRAGFDISESA 74 Query: 80 ITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVF 139 I +SSDSTY RA+LVG+LNT++VA+ GI TATIIGF+IGIGRLS+NWLI K+CTVYVEVF Sbjct: 75 IAYSSDSTYGRAILVGLLNTVIVAIVGIITATIIGFVIGIGRLSKNWLIRKICTVYVEVF 134 Query: 140 RNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVI 199 RNIPPLLVIFFWY GVL+VLP PR+S+ LPF +LN RG FP+ ++ G + +AL++ Sbjct: 135 RNIPPLLVIFFWYSGVLAVLPAPRDSINLPFGSFLNQRGFYFPRAVWGDGSWLIFVALLV 194 Query: 200 AIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNL 259 I + +AR A +RQ ATGQ F WT+ ALIVGLPLL + +SGFPL+FD P FNL Sbjct: 195 GIAMAWFVARKARQRQMATGQQFPVFWTSAALIVGLPLLAYALSGFPLSFDYPKQSTFNL 254 Query: 260 TGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVV 319 TGG V PEF+SL+LALS YTA+FIAEIVR GIRGV GQ+EAAGALGL S+ RLVVV Sbjct: 255 TGGFQVRPEFLSLYLALSCYTAAFIAEIVRAGIRGVSAGQTEAAGALGLRSGSILRLVVV 314 Query: 320 PQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLS 379 PQA+RI+IPPLTSQYLNLTKNSSLAIAIG+ DL A GT+LNQ+GQA+E V I ++YL+ Sbjct: 315 PQAMRIVIPPLTSQYLNLTKNSSLAIAIGYPDLTATAGTVLNQTGQAVEGVVIMMVIYLA 374 Query: 380 LSILTSLFMNWFNAKMALVER 400 +S+LTSL MNWFNAKMALVER Sbjct: 375 ISLLTSLVMNWFNAKMALVER 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: 646 Number of extensions: 31 Number of successful extensions: 1 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 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