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 GFF196 PGA1_c02000 glutamate/glutamine/aspartate/asparagine transport system permease protein BztC
Query= TCDB::Q9I404 (222 letters) >FitnessBrowser__Phaeo:GFF196 Length = 432 Score = 113 bits (283), Expect = 5e-30 Identities = 69/210 (32%), Positives = 111/210 (52%), Gaps = 12/210 (5%) Query: 17 GMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIPLLLVITWFYFA 76 G ++ + L V V V LG LAL R S+ L+ I ++ + R +PL+ ++ F Sbjct: 224 GFMLNMMLGVTCVSLSVPLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLL----FV 279 Query: 77 VPFILRWITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAIPKGQMGAAQALGMTYG 136 +L + D V F ++ +F AAY E++R G+ A+PKGQ AA +LG+ Y Sbjct: 280 ASVMLSYFFPPDATVDLFLRVVIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYP 339 Query: 137 QTMRLVILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLMDFLNSARSRGDIIGQAN---- 192 Q MRL+ILPQA + P ++ ++ LF+DT+LV + + D + RG I+ Sbjct: 340 QAMRLIILPQALKISIPGIVNVAVGLFKDTTLVSVISMFDLVGMI--RGPILASTEWNGV 397 Query: 193 --EFLIFAGLVYFVVSFTASFAVKRLQKRL 220 E L FA ++F+V + S + L++RL Sbjct: 398 YWELLGFAAFLFFIVCYGISQYSQWLERRL 427 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: 247 Number of extensions: 9 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: 432 Length adjustment: 27 Effective length of query: 195 Effective length of database: 405 Effective search space: 78975 Effective search space used: 78975 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: 48 (23.1 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