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 GFF3832 PGA1_262p02360 putative histidine-binding periplasmic protein
Query= TCDB::Q9HU31 (250 letters) >FitnessBrowser__Phaeo:GFF3832 Length = 259 Score = 183 bits (465), Expect = 3e-51 Identities = 104/256 (40%), Positives = 152/256 (59%), Gaps = 8/256 (3%) Query: 1 MKNYKKILLAAAATLAFALDASAADKLRIGTEGA-YPPFNGIDASGQAVGFDLDIGKALC 59 + N K +LAAA T+A + A+ ++IG YPPF +D+SGQ VG+++D+ A+C Sbjct: 4 ISNLKSTVLAAA-TVAATCAVAQAEPVKIGVAAEPYPPFASLDSSGQWVGWEIDVINAVC 62 Query: 60 AKMKTECEVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPK 119 A + +C + WDGIIP+L ++ D I+ASMSIT+ER + +DF+DPYY VA K Sbjct: 63 AAAELDCVITPVAWDGIIPSLTGQQVDAIMASMSITEERLKTIDFSDPYYNTPAVIVADK 122 Query: 120 SVDFKTDKDSLKGKVIGAQRATIAGTWLEDNMADVVTIKLYDTQENAYLDLSSGRLDGVL 179 S+D + +SL GKV+G Q +TI + +++ D +++Y TQ+ A DL +GR+D Sbjct: 123 SMDIEATPESLAGKVVGIQASTIHQAYAQEHFKD-SELRVYQTQDEANQDLFAGRIDATQ 181 Query: 180 ADKFVQYDWLKSDAGKEFEFKGEPVFD----NDKIGIAVRKGD-PLREKLNAALKEIVAD 234 AD D++ SDAG E KG D +G VRKGD + LN + I+AD Sbjct: 182 ADSIAMADFVGSDAGGCCEIKGAVANDEAILGKGVGAGVRKGDSDVLAALNKGIAAILAD 241 Query: 235 GTYKKINDKYFPFSIY 250 GT+ +I KYF SIY Sbjct: 242 GTHAEITSKYFTTSIY 257 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: 180 Number of extensions: 8 Number of successful extensions: 3 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: 259 Length adjustment: 24 Effective length of query: 226 Effective length of database: 235 Effective search space: 53110 Effective search space used: 53110 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: 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