Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate 17519 b3458 leucine transporter subunit (NCBI)
Query= TCDB::P0AD96 (367 letters) >FitnessBrowser__Keio:17519 Length = 369 Score = 576 bits (1485), Expect = e-169 Identities = 284/369 (76%), Positives = 320/369 (86%), Gaps = 2/369 (0%) Query: 1 MNIKGKALLAGCIALAFSNMALAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKG 60 M K ++AG IALA S+ A+A+DIKVAVVGAMSGP+AQ+GD EF GA QA+ DINAKG Sbjct: 1 MKRNAKTIIAGMIALAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKG 60 Query: 61 GIKGNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMI 120 GIKG+KL V+YDDACDPKQAVAVANK+VNDGIKYVIGHLCSSSTQPASDIYEDEGILMI Sbjct: 61 GIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMI 120 Query: 121 TPAATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARA 180 +P AT PELT RGYQ I+RT GLDS QGPTAAKYILE VKPQRIAI+HDKQQYGEGLAR+ Sbjct: 121 SPGATNPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARS 180 Query: 181 VQDGLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAG 240 VQDGLK NANVVFFDGITAGEKDFS L+ARLKKENIDFVYYGGY+PEMGQ+LRQAR+ G Sbjct: 181 VQDGLKAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVG 240 Query: 241 LKTQFMGPEGVANVSLSNIAGESAEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 300 LKTQFMGPEGV N SLSNIAG++AEG+LVT PK YDQ PAN+ IVDA+KA K+DPSG +V Sbjct: 241 LKTQFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANQGIVDALKADKKDPSGPYV 300 Query: 301 WTTYAALQSLQAGLNQ--SDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWH 358 W TYAA+QSL L + SD+P + K LKAN +TV+GPL WDEKGDLKGF+FGVF WH Sbjct: 301 WITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGFDFGVFQWH 360 Query: 359 ANGTATDAK 367 A+G++T AK Sbjct: 361 ADGSSTAAK 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: 548 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: 367 Length of database: 369 Length adjustment: 30 Effective length of query: 337 Effective length of database: 339 Effective search space: 114243 Effective search space used: 114243 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