Align AapP, 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 AZOBR_RS08670 AZOBR_RS08670 arginine ABC transporter ATP-binding protein
Query= TCDB::Q52815 (257 letters) >FitnessBrowser__azobra:AZOBR_RS08670 Length = 258 Score = 399 bits (1025), Expect = e-116 Identities = 192/257 (74%), Positives = 225/257 (87%) Query: 1 MAEAPAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMI 60 MA+ T + E ++ ++KWYG+FHVL++I+L V +GERIVI GPSGSGKSTMI Sbjct: 1 MAQTAGAARTFAQGEPIIQCQGVHKWYGEFHVLKNIDLSVAKGERIVICGPSGSGKSTMI 60 Query: 61 RCINRLEEHQKGKIVVDGTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIW 120 RC+NRLEEHQKG IVVDG ELT +LK I+ VRREVGMVFQHFNLFPHLT+LENCTLAPIW Sbjct: 61 RCLNRLEEHQKGSIVVDGIELTGNLKNIELVRREVGMVFQHFNLFPHLTVLENCTLAPIW 120 Query: 121 VRKMPKKQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPT 180 VRK PK +AEE+AM +LKRV+I EQA+KYPGQLSGGQQQRVAIARSLCM+PK+MLFDEPT Sbjct: 121 VRKKPKAEAEEMAMRYLKRVRIAEQAHKYPGQLSGGQQQRVAIARSLCMSPKVMLFDEPT 180 Query: 181 SALDPEMIKEVLDTMVGLAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFF 240 SALDPEM+KEVLD M+GLAE+GMTMLCVTHEMGFA+ VA+RVIFMD+G+IVEQN P FF Sbjct: 181 SALDPEMVKEVLDVMIGLAEDGMTMLCVTHEMGFAKSVADRVIFMDRGEIVEQNTPNEFF 240 Query: 241 DNPQHERTKLFLSQILH 257 ++PQ +RTKLFLSQIL+ Sbjct: 241 NHPQSDRTKLFLSQILN 257 Lambda K H 0.321 0.135 0.394 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: 269 Number of extensions: 5 Number of successful extensions: 1 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: 257 Length of database: 258 Length adjustment: 24 Effective length of query: 233 Effective length of database: 234 Effective search space: 54522 Effective search space used: 54522 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 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