Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate 8500097 DvMF_0860 extracellular solute-binding protein family 3 (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__Miya:8500097 Length = 246 Score = 127 bits (318), Expect = 3e-34 Identities = 80/244 (32%), Positives = 127/244 (52%), Gaps = 6/244 (2%) Query: 5 KKFLLAAAVSLVFSANAMAADKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKV 64 KK +L A LV + A A + + +A +PP DA+ +VGF D DA+ + Sbjct: 3 KKIVLTLAALLVTANVAFAEKTIVVAQDATWPPMEFVDANKNLVGFSVDYTDAMAKEAGF 62 Query: 65 ECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAEFK 124 + WDGI L + +D ++SS+SIT+ERK A+DFT PYY + + PK+ Sbjct: 63 KIVHKNVAWDGIFAGLESGSYDAIVSSVSITDERKNAMDFTAPYYEVRQALVVPKTTNV- 121 Query: 125 TDKDSLKGKVIGAQRATLAGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILADKYV 184 T D +KGK +G Q +T ++ G +T K YD A DL +GR+D ++ D V Sbjct: 122 TKLDEMKGKTLGGQISTTGYFTIKKTAG--VTAKSYDEIGLAMEDLFNGRIDGVVCDDPV 179 Query: 185 NYDWLKTEAGRAYEFKGDPVVESDK---IGIAVRKGDNELRNKLNAALKEIVADGTYKKI 241 + + A + K V+E+ + GIAV+KG+ E+ + LN + + A G K++ Sbjct: 180 AASYALQQEQYAAKMKIAFVIETQEKEFYGIAVKKGNKEVLDLLNKGIAAVKAKGIDKQL 239 Query: 242 NDKY 245 +K+ Sbjct: 240 REKW 243 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: 159 Number of extensions: 8 Number of successful extensions: 4 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: 246 Length adjustment: 24 Effective length of query: 227 Effective length of database: 222 Effective search space: 50394 Effective search space used: 50394 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