Align leucine-specific-binding protein LivK (characterized)
to candidate WP_013418499.1 RVAN_RS04095 branched-chain amino acid ABC transporter substrate-binding protein
Query= CharProtDB::CH_107418 (369 letters) >NCBI__GCF_000166055.1:WP_013418499.1 Length = 366 Score = 266 bits (680), Expect = 7e-76 Identities = 145/357 (40%), Positives = 216/357 (60%), Gaps = 4/357 (1%) Query: 6 KTIIAGM--IALAISHTAMADDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIK 63 + I+AG+ + L + A ADDI +A+ G M+G A +G G A+ DINAKGG+ Sbjct: 2 RAILAGLTLLGLGAAAPAWADDISIAIAGPMTGKEATFGAQFKAGGEAAVADINAKGGVL 61 Query: 64 GDKLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPG 123 G +L DD CDPKQA AVA ++ + G+ +V GH CSSS+ PAS +Y ++GI+ ISPG Sbjct: 62 GKQLKLEMGDDQCDPKQARAVAEQLSSSGVAFVAGHFCSSSSIPASSVYNEQGIVQISPG 121 Query: 124 ATNPELT-QRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQ 182 +TNP+LT +R R G D QG A Y+ + ++IAI+HDK YG+GLA + Sbjct: 122 STNPKLTDERPGDFTYRMCGRDDQQGGVAGAYLAKEFADKKIAILHDKTAYGQGLADETK 181 Query: 183 DGLKAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGLK 242 L AA VF++ IT GEKD++A++ +LK+ +D VY GGY+ E G ++RQ R+ G+K Sbjct: 182 KALNAAGKQEVFYEAITPGEKDYTAVVTKLKQNGVDVVYLGGYHTEGGLIIRQMRAQGMK 241 Query: 243 TQFMGPEGVGNASLSNIAGDAAEGMLVTMPKRYDQDPANQGIVDALKADKKDPSGPYVWI 302 T +G + + + L +IAGD EG ++T ++PA + +V+AL+ +P G YV Sbjct: 242 TILVGGDALVSTELGSIAGDDVEGTMMTFSPDPRKNPAAKEVVEALEKKGINPEG-YVVY 300 Query: 303 TYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGFDFGVFQW 359 TYAA+Q+ A A E+ GS E +V +K +T +G +D KGD + ++W Sbjct: 301 TYAAIQTWAQAAEKAGSIEGDKVVVAMKDLEFDTALGKFKFDAKGDPNLPSYVFYRW 357 Lambda K H 0.315 0.133 0.386 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: 388 Number of extensions: 18 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: 369 Length of database: 366 Length adjustment: 30 Effective length of query: 339 Effective length of database: 336 Effective search space: 113904 Effective search space used: 113904 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: 41 (21.5 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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