Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_054254771.1 BN2503_RS00920 ABC transporter permease subunit
Query= reanno::pseudo6_N2E2:Pf6N2E2_2959 (242 letters) >NCBI__GCF_001298675.1:WP_054254771.1 Length = 237 Score = 104 bits (260), Expect = 1e-27 Identities = 74/213 (34%), Positives = 111/213 (52%), Gaps = 5/213 (2%) Query: 25 QGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLLIFY 84 QG +T++L+ SL L +L L A A +S LR PAQ +T +RG P L+ + LI+Y Sbjct: 17 QGLVVTLQLTLYSLGLGAVLALACALALVSPRVWLRWPAQTFTYFMRGTPLLIQVYLIYY 76 Query: 85 SLQT--WLTSLTDFMEWEYIEI-DPFGAGVITLGFIYGAYFTETFRGAILSVPRGQVEAA 141 + W+ + D + W + + +PF +++ AY ET G+I +G+VEAA Sbjct: 77 GVAQLEWVQARWDAV-WPWTQFKEPFFCTLLSFSLNTAAYTAETLAGSIRETNKGEVEAA 135 Query: 142 TAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSII-GLADLVKAAQDAGKS 200 A G+ G R +V P +R LP GN ++ML +++L S + L DL AA Sbjct: 136 RAMGMGHGMLMRRIVLPSAIRRMLPAYGNEVVMMLHSSSLASTVPALLDLTGAASRVYAD 195 Query: 201 TYQLFYFLVLAALIYLLITSASNFILRWLERRY 233 + F + AA IYL IT A + LERR+ Sbjct: 196 FFLPFEAYLFAAAIYLCITFALIGASKLLERRF 228 Lambda K H 0.329 0.142 0.418 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: 171 Number of extensions: 9 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: 242 Length of database: 237 Length adjustment: 23 Effective length of query: 219 Effective length of database: 214 Effective search space: 46866 Effective search space used: 46866 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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