Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_05882 H281DRAFT_05882 amino acid ABC transporter substrate-binding protein, PAAT family
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__Burk376:H281DRAFT_05882 Length = 262 Score = 165 bits (418), Expect = 8e-46 Identities = 92/249 (36%), Positives = 147/249 (59%), Gaps = 6/249 (2%) Query: 8 LLAAAVSLVFSANAMAADKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKVECE 67 L+AA + + + + + L+ GIEAAYPPF +K +GQ+ GFD D+G+A+CAK+ ++C Sbjct: 11 LVAATAASLSTVTTQSQETLRFGIEAAYPPFESKSPTGQLQGFDVDVGNAVCAKLGMKCV 70 Query: 68 VVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAEFKTDK 127 V + +DG+IPAL A+KFD + S+++ITE+RKQ+++FT P Y + +A +++ D Sbjct: 71 WVENAFDGLIPALQARKFDVINSAMNITEKRKQSIEFTKPIYVVPIVMVARRASGLLPDV 130 Query: 128 DSLKGKVIGAQRATLAGTWLEDELG-SDITTKLYDTQENAYLDLTSGRVDAILADKYVNY 186 SL+GK +G +A+ +L+ + +T Y Q+ Y DL +GR+DA + + Sbjct: 131 KSLQGKRVGVLQASSQEDFLKRHWAPAGVTVVPYADQDQVYADLVAGRLDAAVQEAQTVQ 190 Query: 187 D-WLKTEAGRAYEFKG----DPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKKI 241 D +L AG Y G DP + G +RKGD L K++AAL + DGT + Sbjct: 191 DGFLVKPAGHEYAIVGKPLSDPATLGEGTGWGLRKGDKVLVAKVDAALDALKKDGTLSSL 250 Query: 242 NDKYFPFNI 250 + KYF +I Sbjct: 251 SQKYFKQDI 259 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: 150 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: 262 Length adjustment: 24 Effective length of query: 227 Effective length of database: 238 Effective search space: 54026 Effective search space used: 54026 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