Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein
Query= TCDB::P0AD96 (367 letters) >MicrobesOnline__882:206137 Length = 376 Score = 178 bits (452), Expect = 2e-49 Identities = 119/369 (32%), Positives = 190/369 (51%), Gaps = 20/369 (5%) Query: 8 LLAGCIALAFSNMALA---EDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIKG 64 LLA C+ + A A ++V ++ ++G A G E ++N GGI G Sbjct: 7 LLAVCMVTSLLMAATAFAAGPVRVGLMCPLTGKWASEGQDMRNIVELLAEEVNKAGGING 66 Query: 65 NKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPAA 124 NK++++ DD DP+ A A K+ G+ VIG S+ T+ + +IY++ GI I + Sbjct: 67 NKVELIVEDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIAQIATGS 126 Query: 125 TAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQDG 184 T LT +G +L LRT D +QG AAK I K + +A++HD Y +GLA + Sbjct: 127 TNVRLTEKGLKLFLRTCPRDDEQGRVAAKVIKNK-GYKAVALLHDNSSYAKGLADETKAL 185 Query: 185 LKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLKTQ 244 L K +VF+D +T GE+D++ ++ +LK N D +++ GY+PE+G +LRQ Sbjct: 186 LDKDGTKIVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKMEMKWNVP 245 Query: 245 FMGPEGVANVSLSNIAGESAEG----LLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 300 MG + N+ L IAG++A L P+++D A K + A KAK + V Sbjct: 246 MMGGDAANNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEA-KAFLAAYKAKHNALPNS-V 303 Query: 301 WTTYAA------LQSLQAGLNQSDDPAEIAKYLKA--NSVDTVMGPLTWDEKGDLKGFEF 352 W+ A ++++Q G D A IA YLK + + G ++++EKGD G + Sbjct: 304 WSVLAGDAFKVIVEAVQKG--GKADGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGDLY 361 Query: 353 GVFDWHANG 361 V+D +A G Sbjct: 362 RVYDVNAEG 370 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: 339 Number of extensions: 21 Number of successful extensions: 4 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: 376 Length adjustment: 30 Effective length of query: 337 Effective length of database: 346 Effective search space: 116602 Effective search space used: 116602 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: 49 (23.5 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