Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate AO356_08500 AO356_08500 amino acid ABC transporter substrate-binding protein
Query= TCDB::P0AD96 (367 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_08500 Length = 378 Score = 279 bits (713), Expect = 1e-79 Identities = 150/363 (41%), Positives = 222/363 (61%), Gaps = 8/363 (2%) Query: 6 KALLAGCIALAFSNMALAE-DIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKG 64 K LA +A A A A+ D+K V G M+G A +G+Q GA+ A IN GG+ G Sbjct: 8 KGFLALAVAAALGVSAFAQADVKFGVAGPMTGANAAFGEQYMKGAQAAADAINKAGGVNG 67 Query: 65 NKLQIVKYDDACDPKQAVAVANKVVN-DGIKYVIGHLCSSSTQPASDIYEDEGILMITPA 123 K+ +V DDAC+PKQAVAVAN++V+ D + V+GH CSS+T PAS++Y++ GI+ ITP Sbjct: 68 EKIVLVAGDDACEPKQAVAVANRLVDQDKVIGVVGHFCSSNTIPASEVYDEAGIIAITPG 127 Query: 124 ATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQD 183 +T P++T RG + R G D QG A YI++ +K +++A++HDK YG+GLA A + Sbjct: 128 STNPQVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVLHDKDTYGQGLADATKA 187 Query: 184 GLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLK- 242 L K V ++G+T GEKDFS +V +++ D VY+GG HPE G ++RQ R GLK Sbjct: 188 QLAKRGVKEVLYEGLTRGEKDFSAVVTKIRSVGADVVYFGGLHPEAGPLVRQLREQGLKD 247 Query: 243 TQFMGPEGVANVSLSNIAG--ESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 300 +FM +G+ L AG + +G+ +T + +P +K +V+ + +P G + Sbjct: 248 VKFMSDDGIVTDELVTTAGGAQYVDGVYMTFGADPRLLPDSKAVVEEFRKNGTEPEG-YT 306 Query: 301 WTTYAALQSLQAGLN--QSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWH 358 YA++Q+L AG N +S+ + AK+LKAN V TVMG WD KGDLK ++ V+ W Sbjct: 307 LYAYASVQALAAGFNGAKSNKGEDAAKWLKANPVQTVMGKKEWDTKGDLKVSDYVVYQWD 366 Query: 359 ANG 361 +G Sbjct: 367 KDG 369 Lambda K H 0.314 0.133 0.380 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: 428 Number of extensions: 23 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: 367 Length of database: 378 Length adjustment: 30 Effective length of query: 337 Effective length of database: 348 Effective search space: 117276 Effective search space used: 117276 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: 42 (22.0 bits) S2: 50 (23.9 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