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 BPHYT_RS08555 BPHYT_RS08555 ABC transporter permease
Query= TCDB::Q9I404 (222 letters) >FitnessBrowser__BFirm:BPHYT_RS08555 Length = 219 Score = 110 bits (276), Expect = 2e-29 Identities = 77/222 (34%), Positives = 117/222 (52%), Gaps = 7/222 (3%) Query: 1 MMDFSGIVPALPSLWEGMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNY 60 M S +V +LP L +G ++T+K VL ++ G+ G VLALM +SH+++L+ IA YV+ Sbjct: 1 MSTTSLLVESLPVLAQGAVLTVKFAVLSMIFGLIAGAVLALMGVSHNRVLNWIARIYVSV 60 Query: 61 FRSIPLLLVITWFYFAVPFILRWITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAI 120 R PLL+ I Y+ +P I+ + TP G ++A AAY E +R I I Sbjct: 61 MRGTPLLVQIFVIYYGLPSF--GISLDPTPAG-----VIALSANVAAYLSESMRGAILGI 113 Query: 121 PKGQMGAAQALGMTYGQTMRLVILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLMDFLNS 180 GQ AA +LG++ QT+R VI PQA R P + I L +DTSLV + + + L S Sbjct: 114 HNGQWLAAYSLGLSRRQTLRYVIAPQALRIAVPSMSNSLISLIKDTSLVSVITVTELLRS 173 Query: 181 ARSRGDIIGQANEFLIFAGLVYFVVSFTASFAVKRLQKRLTV 222 A+ Q + A VY+V+ + ++RL + Sbjct: 174 AQEIIASTYQPLPLYLAAAAVYWVLCQVLESVQRWYERRLAL 215 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: 120 Number of extensions: 5 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: 219 Length adjustment: 22 Effective length of query: 200 Effective length of database: 197 Effective search space: 39400 Effective search space used: 39400 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