Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate Pf6N2E2_3856 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3856 Length = 251 Score = 390 bits (1003), Expect = e-113 Identities = 186/251 (74%), Positives = 218/251 (86%), Gaps = 1/251 (0%) Query: 1 MKNYKKILLAAAATLAFALDASAADKLRIGTEGAYPPFNGIDASGQAVGFDLDIGKALCA 60 M+ Y+K LLAAA +L F+ A A +KL++G E AYPPFN DASGQ VGFD DIG ALCA Sbjct: 1 MQTYRKFLLAAAVSLVFSTSAMAVEKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCA 60 Query: 61 KMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKS 120 KMK ECEVVTS+WDGIIPAL AKKFDF+++S+S+ DERKQAVDFTDPYY+NKLQF+APK+ Sbjct: 61 KMKVECEVVTSNWDGIIPALMAKKFDFLISSLSVNDERKQAVDFTDPYYSNKLQFIAPKN 120 Query: 121 VDFKTDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVLA 180 VDFK DK+SLKGKVIGAQR+T+AGTWLED + +T KLYDTQENAYLDL+SGR+D +LA Sbjct: 121 VDFKVDKESLKGKVIGAQRSTLAGTWLEDELGSDITAKLYDTQENAYLDLTSGRVDAILA 180 Query: 181 DKFVQYDWLKSDAGKEFEFKGEPVFDNDKIGIAVRKG-DPLREKLNAALKEIVADGTYKK 239 DK+V YDWLK++AG+ +EFKG+PV + DKI IAVRKG D LR KLNAALKEI+ADGTYKK Sbjct: 181 DKYVNYDWLKTEAGRAYEFKGDPVVEGDKIAIAVRKGNDELRNKLNAALKEILADGTYKK 240 Query: 240 INDKYFPFSIY 250 INDKYFPFSIY Sbjct: 241 INDKYFPFSIY 251 Lambda K H 0.317 0.135 0.392 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: 309 Number of extensions: 10 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: 250 Length of database: 251 Length adjustment: 24 Effective length of query: 226 Effective length of database: 227 Effective search space: 51302 Effective search space used: 51302 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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