Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate H281DRAFT_05872 H281DRAFT_05872 amino acid ABC transporter membrane protein 2, PAAT family
Query= TCDB::Q9I404 (222 letters) >FitnessBrowser__Burk376:H281DRAFT_05872 Length = 214 Score = 114 bits (284), Expect = 2e-30 Identities = 63/210 (30%), Positives = 111/210 (52%), Gaps = 7/210 (3%) Query: 10 ALPSLWEGMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIPLLLV 69 +L L +G++ TL L + ++G +G + A++R IA Y FR P+L+ Sbjct: 9 SLSILLQGLVTTLLLSIAAIVGSTLIGLLAAVLRSFGPWGTDRIAKLYTELFRGTPVLIT 68 Query: 70 ITWFYFAVPFILRWITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAIPKGQMGAAQ 129 + + YF V + + F + ++ +++ AY E+ RAGI+++PKGQ +Q Sbjct: 69 LMFIYFGVSYF-------GYAIDVFAAGVIGLSVYQGAYIAEVFRAGIESVPKGQWEVSQ 121 Query: 130 ALGMTYGQTMRLVILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLMDFLNSARSRGDIIG 189 LG++ QT V+LPQ R + P L+ Q + L +DTS+V +G+ + ++ ++ D +G Sbjct: 122 ILGLSRIQTFASVVLPQTGRIVLPPLVGQYLSLIKDTSIVSMIGMSELMHGGQAIVDRVG 181 Query: 190 QANEFLIFAGLVYFVVSFTASFAVKRLQKR 219 + E L+YFVV F S V+ +R Sbjct: 182 KPVEIYGLVALIYFVVCFPLSQWVRHHDRR 211 Lambda K H 0.331 0.143 0.426 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: 129 Number of extensions: 7 Number of successful extensions: 2 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: 222 Length of database: 214 Length adjustment: 22 Effective length of query: 200 Effective length of database: 192 Effective search space: 38400 Effective search space used: 38400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 45 (21.9 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