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_004141766.1 Mesci_2580 binding-protein-dependent transport system inner membrane protein
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000185905.1:YP_004141766.1 Length = 387 Score = 205 bits (522), Expect = 2e-57 Identities = 130/383 (33%), Positives = 202/383 (52%), Gaps = 10/383 (2%) Query: 20 SAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSL 79 S + + K R+ Q+L + + V NLA SGF FL G+++ SL Sbjct: 3 SLLRNQKVRNALLQVLYVGSIAAMVLAGIVIARRNLADQGITSGFDFLFKSTGWDVNFSL 62 Query: 80 ITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVF 139 + +++ Y L+GI+NTL + G+ ATI+G ++G+ R S N L L YV++F Sbjct: 63 LPATANDPYWWYFLIGIINTLFLGSVGLILATIVGTIVGLARTSSNDLARLLGRTYVDIF 122 Query: 140 RNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVI 199 RNIP +L +FFWY +++ LP PR S + L +RGL P P + A A + Sbjct: 123 RNIPLILQVFFWY-AIITHLPTPR-SAHEAWGFLLTSRGLYIPFPNVGSAAFA---AATV 177 Query: 200 AIVASIIIARWAHKRQAAT---GQPFHTVWTAIALIVGLPLLVFVVSGFPLT--FDVPVA 254 A++A+I++ W + GQ + A A + ++ + P T D P Sbjct: 178 AVIAAIVLPAWLGRTSLLAQPIGQRRTIQFAAAAAALACATIILALGRLPDTPLLDFPAL 237 Query: 255 GKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVT 314 NL GG + PEF +L +A++ Y S+IAEIVRGG + V GQ EAA +LGL P V Sbjct: 238 QGLNLRGGLRIPPEFATLAIAIAIYGGSYIAEIVRGGFKSVGTGQVEAALSLGLSPWRVF 297 Query: 315 RLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWG 374 LV +P ALR ++P L +QY+ L K +++ IA+GF+D + +N SGQ +E + I Sbjct: 298 TLVRLPLALRAMLPILANQYVWLMKATTMGIAVGFTDFFMIVALTINHSGQTLEAIGILM 357 Query: 375 IVYLSLSILTSLFMNWFNAKMAL 397 +L++++ + N N +AL Sbjct: 358 AGFLAINLSLAAVFNRINKAIAL 380 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: 434 Number of extensions: 22 Number of successful extensions: 4 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: 387 Length adjustment: 31 Effective length of query: 369 Effective length of database: 356 Effective search space: 131364 Effective search space used: 131364 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