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_008511689.1 BIBO1_RS19985 amino acid ABC transporter permease
Query= TCDB::Q52813 (400 letters) >NCBI__GCF_000182725.1:WP_008511689.1 Length = 323 Score = 90.9 bits (224), Expect = 5e-23 Identities = 89/290 (30%), Positives = 136/290 (46%), Gaps = 43/290 (14%) Query: 98 NTLLVAVTGIFTATIIGFLIG--IGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGV 155 N ++ F+ ++I FL + RLSRN ++ V+ E+F LL+IFF+ Sbjct: 53 NPVVARALSAFSISLILFLNWKLLKRLSRN---QQVVAVWTELF----VLLMIFFY---- 101 Query: 156 LSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDT---GMIAVGIALVIAIVASIIIARWAH 212 S L FS + T I++ IA +IA++ +I A Sbjct: 102 ---------SFDLSFSFIARKISFLITQGTVTTLYISAISIAIATIIALIGAI-----AK 147 Query: 213 KRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSL 272 Q T +T+ L GLPLL+ + + + +P G + G G Sbjct: 148 LSQNGVIYGLSTFYTS--LFRGLPLLMQI---YIIYLGLPQIGY--VIGAIPAG------ 194 Query: 273 FLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRIIIPPLTS 332 LALS +++ EI R GI +P GQ EAA ALGL + LV++PQA+RIIIPP + Sbjct: 195 ILALSLCYGAYMTEIFRAGIESIPHGQKEAATALGLGSAQTMWLVILPQAMRIIIPPTGN 254 Query: 333 QYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSI 382 Q++ + K+SSL IG +L+ V T + IE++ ++Y LSI Sbjct: 255 QFIAMLKDSSLVSVIGVWELMYVARTQGQTEFRHIEMLITASMIYWILSI 304 Score = 48.1 bits (113), Expect = 4e-10 Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 6/86 (6%) Query: 95 GILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLG 154 G + TL ++ I ATII + I +LS+N +I L T Y +FR +P L+ I+ YLG Sbjct: 121 GTVTTLYISAISIAIATIIALIGAIAKLSQNGVIYGLSTFYTSLFRGLPLLMQIYIIYLG 180 Query: 155 ------VLSVLPQPRESVGLPFSMYL 174 V+ +P ++ L + Y+ Sbjct: 181 LPQIGYVIGAIPAGILALSLCYGAYM 206 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: 359 Number of extensions: 23 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 400 Length of database: 323 Length adjustment: 29 Effective length of query: 371 Effective length of database: 294 Effective search space: 109074 Effective search space used: 109074 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: 49 (23.5 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