Align ABC transporter for L-Arginine, substrate-binding component (characterized)
to candidate PP_4486 PP_4486 lysine / arginine / ornithine ABC transporter - periplasmic binding protein
Query= reanno::WCS417:GFF4245 (261 letters) >FitnessBrowser__Putida:PP_4486 Length = 261 Score = 453 bits (1165), Expect = e-132 Identities = 226/261 (86%), Positives = 239/261 (91%) Query: 1 MKKLVLLGALALSVLSMQAFAEGKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60 MKKL LLGALALSV S+ + A KPLKIGIEAAYPPFA K PDGSI GFDYDIGNALCEE Sbjct: 1 MKKLALLGALALSVFSLVSQAAEKPLKIGIEAAYPPFAFKQPDGSIAGFDYDIGNALCEE 60 Query: 61 MKVKCTWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNRYYLTPARLVLKEGT 120 MK KCTWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFT RYYLTPARLV+K+GT Sbjct: 61 MKTKCTWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTKRYYLTPARLVMKDGT 120 Query: 121 AVSDSLDELKGKKIGVQRGSIHDRFAKEVLAPKGATIVPYSSQNEIYLDVEAGRLDGTVA 180 VSDSLDELKGKKIGVQRGSIHDRFAKEVL KGAT+VPY +QNEIYLDV AGRLDGTVA Sbjct: 121 TVSDSLDELKGKKIGVQRGSIHDRFAKEVLGAKGATVVPYGTQNEIYLDVAAGRLDGTVA 180 Query: 181 DATLLQEGFLDTPAGKGYAFTGPAFTDAKYFGDGIGIAVRKGDKENLDRINAAIAAIRAN 240 DATLL++GFL T AGKG+AF GPAFTDAKYFGDGIGIAVRKGDK N+DRINAAI AIRAN Sbjct: 181 DATLLEDGFLKTDAGKGFAFVGPAFTDAKYFGDGIGIAVRKGDKANVDRINAAIDAIRAN 240 Query: 241 GKYKEIEKKYFNFDIYGPEAQ 261 GKYKEIE KYFNFDIYGP+++ Sbjct: 241 GKYKEIESKYFNFDIYGPDSK 261 Lambda K H 0.317 0.137 0.390 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: 325 Number of extensions: 10 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: 261 Length of database: 261 Length adjustment: 25 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 (21.6 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