Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate Ac3H11_3325 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3325 Length = 253 Score = 107 bits (267), Expect = 2e-28 Identities = 79/254 (31%), Positives = 133/254 (52%), Gaps = 16/254 (6%) Query: 1 MQTYKKFLLAAAVSLVFSANAMAADKLK------MGIEAAYPPFNNKDASGQVVGFDKDI 54 M+ +K A A+ F+A A D++K + E + PFN + + + GF+ ++ Sbjct: 1 MKLFKAVATALALCAAFAAQARTLDEVKKDGKILIATEGQFAPFNFFNGT-TLTGFEVEV 59 Query: 55 GDALCAKMKVECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQ 114 + + KM + + T +D ++ L ++D +I+S ITEER +AV FT+P+Y + Sbjct: 60 AELVAKKMGLTIQWKTLGFDALLTGLRQDRWDLVIASHGITEERAKAVTFTEPHYCSGGM 119 Query: 115 FIAPKSAEFKTDKDSLKGKVIGAQRATLAGTWLED--ELGSDITTKLYDTQENAYLDLTS 172 IA A K+ KD L GK++ Q T ++LE+ ++ S K + T +A L S Sbjct: 120 IIAMDPA-IKSAKD-LAGKIVAVQTGT---SYLENVQKVSSIKEMKNFPTDVDARSALNS 174 Query: 173 GRVDAILADKYVNYDWLKTEAGRAYEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEI 232 RVDA + D++V + G FK ++ ++I AV KG++ L N AL E+ Sbjct: 175 RRVDAWVTDRFVAKAVAEKNPGAG--FKLGDMLFIERIAAAVAKGNSSLAGGWNKALAEV 232 Query: 233 VADGTYKKINDKYF 246 +ADG+Y ++ KYF Sbjct: 233 MADGSYAALSKKYF 246 Lambda K H 0.316 0.133 0.381 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: 137 Number of extensions: 6 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: 251 Length of database: 253 Length adjustment: 24 Effective length of query: 227 Effective length of database: 229 Effective search space: 51983 Effective search space used: 51983 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: 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