Align Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate AO353_13340 AO353_13340 amino acid ABC transporter substrate-binding protein
Query= TCDB::P0AD96 (367 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13340 Length = 377 Score = 286 bits (731), Expect = 8e-82 Identities = 155/363 (42%), Positives = 221/363 (60%), Gaps = 7/363 (1%) Query: 4 KGKALLAGCIALAFSNMALAEDIKVAVVGAMSGPVAQYGDQEFTGAEQAVADINAKGGIK 63 KG LA AL S+ A D+K+ V G M+GP A +G Q GA+ A INAKGGI Sbjct: 8 KGFVALAVAAALGVSSFVQA-DVKLGVAGPMTGPSASFGLQYMKGAQAAADAINAKGGIN 66 Query: 64 GNKLQIVKYDDACDPKQAVAVANKVVNDGIKYVIGHLCSSSTQPASDIYEDEGILMITPA 123 G K+ +V+ DDAC+PKQAVAVANK+V D + V+GH CSSST PAS++Y D GI+ ITP Sbjct: 67 GEKIVLVQGDDACEPKQAVAVANKMVQDKVIGVVGHFCSSSTIPASEVYSDAGIIAITPG 126 Query: 124 ATAPELTARGYQLILRTTGLDSDQGPTAAKYILEKVKPQRIAIVHDKQQYGEGLARAVQD 183 +T P +T RG ++R G D QG A YI++ +K +++A+++DK YG+GLA A Sbjct: 127 STNPTVTERGLPAMMRMCGRDDQQGIVAGNYIVDVLKGKKVAVINDKDTYGKGLADATAK 186 Query: 184 GLKKGNANVVFFDGITAGEKDFSTLVARLKKENIDFVYYGGYHPEMGQILRQARAAGLK- 242 L V +G+T GEKDFS L+ +++ D +Y+GG HPE G ++ Q R GLK Sbjct: 187 QLTARGVKPVLEEGLTRGEKDFSALITKVRSVGADVLYFGGLHPEAGPLVHQLREQGLKD 246 Query: 243 TQFMGPEGVANVSLSNIAGES--AEGLLVTKPKNYDQVPANKPIVDAIKAKKQDPSGAFV 300 +FM +G+ + AG + +G+ +T + +P +K +VD + +P G + Sbjct: 247 VKFMSDDGIVTDEMVTTAGGAPYVDGVYMTFGADPRLIPDSKAVVDTFRKSGYEPEG-YT 305 Query: 301 WTTYAALQSLQAGLN--QSDDPAEIAKYLKANSVDTVMGPLTWDEKGDLKGFEFGVFDWH 358 YA++Q+L AG N +S+ E AK+LKA+ V+TVMG WD KGDLK ++ V+ W Sbjct: 306 LYAYASVQALAAGFNGAKSNKGEEAAKWLKAHPVETVMGKKEWDSKGDLKISDYVVYQWD 365 Query: 359 ANG 361 A G Sbjct: 366 AAG 368 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: 434 Number of extensions: 23 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: 377 Length adjustment: 30 Effective length of query: 337 Effective length of database: 347 Effective search space: 116939 Effective search space used: 116939 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