Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS00160 BPHYT_RS00160 ABC transporter substrate-binding protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2958 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS00160 Length = 262 Score = 212 bits (540), Expect = 6e-60 Identities = 118/258 (45%), Positives = 158/258 (61%), Gaps = 4/258 (1%) Query: 3 KALLTLSALALCMAAGVAT--AKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAIC 60 K L L ALA A+ A+ A LRFG++ Y PFESK +G L G DID+GNA+C Sbjct: 2 KLLKPLLALACAFASLAASSGASAADTLRFGLEAQYPPFESKGPNGELQGLDIDVGNAVC 61 Query: 61 AELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKAIDFSSELFSGPTAYVFKK 120 + CKWVE+ FDG+IP L+ KFD + S+M T AR +AIDF++ ++ PT + K+ Sbjct: 62 VAAHMTCKWVETSFDGLIPALQGRKFDAINSAMNATDARRQAIDFTTVVYRVPTQLIAKR 121 Query: 121 GSGLSEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYADLTSGRLDAA 180 SGL ASLKGK VG Q +IQE YAKA + AGV YQ+Q+QVY DL +GRLDA Sbjct: 122 DSGLLPTPASLKGKRVGVLQASIQETYAKAHWESAGVTVVPYQDQNQVYTDLVAGRLDAT 181 Query: 181 IQDMLQAELGFLKSPKGEGYE-VSKPV-DSELLPSKTAIGIRKGNSELKALLNKGIKALH 238 + + GFL P GEGY V +PV D ++L S A GIRKG++ L+ LN I + Sbjct: 182 LVLAPAGQTGFLSKPSGEGYAFVGEPVRDDKILGSGIAYGIRKGDTALRDRLNAAIAKVQ 241 Query: 239 DDGKYAEIQKKHFGDLNL 256 DG + K+ G++++ Sbjct: 242 ADGTVKTLAAKYLGNIDV 259 Lambda K H 0.313 0.132 0.368 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: 185 Number of extensions: 8 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: 260 Length of database: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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