Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate PP_4486 PP_4486 lysine / arginine / ornithine ABC transporter - periplasmic binding protein
Query= uniprot:A0A1N7UK26 (258 letters) >FitnessBrowser__Putida:PP_4486 Length = 261 Score = 189 bits (480), Expect = 5e-53 Identities = 100/253 (39%), Positives = 151/253 (59%), Gaps = 3/253 (1%) Query: 6 SLFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLEVK 65 +L AL L + + K ++ G+ YPPF DGS+ GFD ++GNA+C +++ K Sbjct: 5 ALLGALALSVFSLVSQAAEKPLKIGIEAAYPPFAFKQPDGSIAGFDYDIGNALCEEMKTK 64 Query: 66 CTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADFGD 125 CTWV EFDG+IPAL+ RK DAI+SSM++T R+K +DF+ R +L+P ++ + D Sbjct: 65 CTWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTKRYYLTPARLVMKDGTTVSD 124 Query: 126 TPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDKLE 185 + + L GK++GV +GS+ + +A+ L GA + Y +Q++ Y D+ GRLD T+ D Sbjct: 125 SLDELKGKKIGVQRGSIHDRFAKEVLGAKGATVVPYGTQNEIYLDVAAGRLDGTVADATL 184 Query: 186 AQLNFLSKPEGSDFK-TGPAFKDPTLPLD-IAMGLRKNDQALRALINKGIAAVQADGTYA 243 + FL G F GPAF D D I + +RK D+A IN I A++A+G Y Sbjct: 185 LEDGFLKTDAGKGFAFVGPAFTDAKYFGDGIGIAVRKGDKANVDRINAAIDAIRANGKYK 244 Query: 244 QIQKKYFGDQDIY 256 +I+ KYF + DIY Sbjct: 245 EIESKYF-NFDIY 256 Lambda K H 0.319 0.135 0.393 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: 199 Number of extensions: 11 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: 258 Length of database: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 (21.8 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