Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate PP_0656 PP_0656 putative Amino acid ABC transporter, permease protein
Query= reanno::pseudo5_N2C3_1:AO356_09905 (231 letters) >FitnessBrowser__Putida:PP_0656 Length = 273 Score = 127 bits (320), Expect = 2e-34 Identities = 82/230 (35%), Positives = 128/230 (55%), Gaps = 18/230 (7%) Query: 4 DLHGF--GP-ALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVR 60 +L GF GP GA +T+ L L ++ + ++LG ALA+ S L + Y++ R Sbjct: 57 NLAGFKLGPNGFLQGAALTLFLCLCSMVVSVLLGFAAALARLSNSAVLVGVASFYTSFFR 116 Query: 61 GIPELLWVLLIYFGTVNLMRALGEYLGMPDLAL--NAFAAGVIALGLCFGAYATEVFRGA 118 G P L+ +LLIY LG+P + L A +AG+IAL L +GAY +E+FR Sbjct: 117 GTPLLIQILLIY-------------LGLPQVGLVPGAISAGIIALSLNYGAYLSEIFRAG 163 Query: 119 ILAIPKGHREAGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEE 178 IL + +G REA +ALG+ +IF +I+PQ R+ +P N F+ ++KD++L+SV+G+ E Sbjct: 164 ILGVARGQREAALALGMRTPQIFCHIILPQAMRVIIPPTANQFISMLKDSSLISVMGVWE 223 Query: 179 IMRHAQIGVTVSKQPFTFYMVAALMYLGLTVLAMLGMHLLERRAARGFAR 228 +M AQ S + AA++Y L++L L LER + + R Sbjct: 224 VMFLAQSYGRSSYRYLEMLTTAAVIYWVLSILLELLQARLERHFGKAYQR 273 Lambda K H 0.329 0.143 0.435 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: 231 Length of database: 273 Length adjustment: 24 Effective length of query: 207 Effective length of database: 249 Effective search space: 51543 Effective search space used: 51543 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 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