Align leucine-specific-binding protein LivK (characterized)
to candidate BPHYT_RS26525 BPHYT_RS26525 amino acid ABC transporter substrate-binding protein
Query= CharProtDB::CH_107418 (369 letters) >FitnessBrowser__BFirm:BPHYT_RS26525 Length = 383 Score = 191 bits (486), Expect = 2e-53 Identities = 118/357 (33%), Positives = 190/357 (53%), Gaps = 6/357 (1%) Query: 7 TIIAGMIALAISHTAMADDIKVAVVGAMSGPIAQWG-DMEFNGARQAIKDINAKGGIKGD 65 T+ A + S A +K+ VG ++GP+A+ G D+++ GA+ A+ + NAK + G Sbjct: 11 TVCALATYMPFSWAADPQIVKIGFVGPLTGPVARVGKDLQY-GAQLALDEENAKNPMIGG 69 Query: 66 KLVGVEYD---DACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISP 122 K V D D DP+ A+ VA K+V+DG+ VIGH S + PAS +Y + MI+P Sbjct: 70 KPVKFVLDVQDDQADPRVAIQVAQKLVDDGVVGVIGHYNSGCSIPASTVYHQANVAMITP 129 Query: 123 GATNPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRIAIIHDKQQYGEGLARSVQ 182 G+TNP+LT++G++++ RT G D G A +++E +K +RIAII D+ +G+GLA + + Sbjct: 130 GSTNPQLTKQGFKNVFRTMGHDGIGGVVAGHFVVEQMKAKRIAIIDDRTAFGQGLADAFE 189 Query: 183 DGLKAANANVVFFDGITAGEKDFSALIARLKKENIDFVYYGGYYPEMGQMLRQARSVGLK 242 G+K AN N+V + DF A++ LK +N+D +++GG + +++Q RS+G+ Sbjct: 190 KGVKEANGNIVDREFTNDKAIDFRAILTTLKSKNVDLIFFGGLDEQGAMLVKQMRSLGMS 249 Query: 243 TQFMGPEGVGNASLSNIAGDAAEGMLVTMP-KRYDQDPANQGIVDALKADKKDPSGPYVW 301 TQ G + + + IAG A G P D+ PA Q KA Y Sbjct: 250 TQLFGAGALKSNAFLQIAGTAGNGTQDLEPGPALDKLPAAQAFGKRYKARFNQDVELYAP 309 Query: 302 ITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKGFDFGVFQ 358 +Y A ++ A+ S + +V L V G + +D GDL + +FQ Sbjct: 310 FSYDAALAMLKAIHTADSLDRAKIVDSLAKVTVTGVTGNITFDPYGDLIKPPYTLFQ 366 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: 381 Number of extensions: 13 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: 369 Length of database: 383 Length adjustment: 30 Effective length of query: 339 Effective length of database: 353 Effective search space: 119667 Effective search space used: 119667 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: 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