Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate AZOBR_RS00680 AZOBR_RS00680 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09905 (231 letters) >FitnessBrowser__azobra:AZOBR_RS00680 Length = 234 Score = 196 bits (498), Expect = 3e-55 Identities = 105/225 (46%), Positives = 146/225 (64%), Gaps = 1/225 (0%) Query: 6 HGFGPALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVRGIPEL 65 +G+G L GA MTV +++SA LGLV G LGA AK S L + Y+T+VRG+PEL Sbjct: 10 NGWGGQLLGGAAMTVAVSVSAFVLGLVFGSLGASAKLSRNLALTGVAEVYTTVVRGVPEL 69 Query: 66 LWVLLIYFGTVNLMRALGEYLGMPD-LALNAFAAGVIALGLCFGAYATEVFRGAILAIPK 124 L + L++FG + A+G G + LNAF+ GV+A+GL GAY+TEV RGA+ A+P Sbjct: 70 LVIYLLFFGGSGAVMAVGRVFGYEGYIELNAFSIGVLAVGLISGAYSTEVIRGAVQAVPH 129 Query: 125 GHREAGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHAQ 184 G EA A G+S+W I R+++PQ R ALPGLGN++ + +KDTAL+SV L EIMR + Sbjct: 130 GQIEAARACGMSRWLILRRILVPQTLRYALPGLGNVWQLTLKDTALISVTALAEIMRVSH 189 Query: 185 IGVTVSKQPFTFYMVAALMYLGLTVLAMLGMHLLERRAARGFARS 229 + ++QPF FY AA++YL LT ++ + ER A RG R+ Sbjct: 190 VAAGSTRQPFLFYTTAAVLYLLLTTVSTVAFERAERYANRGVRRA 234 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: 179 Number of extensions: 10 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: 234 Length adjustment: 23 Effective length of query: 208 Effective length of database: 211 Effective search space: 43888 Effective search space used: 43888 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