Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_045585058.1 AL072_RS29535 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_001305595.1:WP_045585058.1 Length = 366 Score = 309 bits (791), Expect = 9e-89 Identities = 157/358 (43%), Positives = 229/358 (63%), Gaps = 10/358 (2%) Query: 11 LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70 L AA+A ++ + AD I +A AGP+TG A +G+ + G A+ IN AGGV G + Sbjct: 7 LLAAIAATALSATAAKAD-IAVATAGPITGQYATFGEQMKKGMEQAVADINAAGGVLGQK 65 Query: 71 LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130 L+ + DDACDPKQAVAVAN++ GVKFV GH CS S+ PA+ +Y +EG+L I+P++T Sbjct: 66 LKLEVGDDACDPKQAVAVANQLAKAGVKFVAGHFCSGSSIPASQVYAEEGMLQISPASTN 125 Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190 P++T +G K +FR G D+ QG +AGK++ E+YK K +A+LHDK YG+G+A E +K + Sbjct: 126 PKLTEQGLKNVFRVCGRDDQQGMIAGKYLLEKYKGKNVAILHDKSAYGKGLADETQKALN 185 Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250 G K A++E AG+KD++AL+SKLK+A V VY GGYH E GLL RQ K GL A + Sbjct: 186 AGGQKEAIYEAYTAGEKDYSALVSKLKQANVDAVYVGGYHTEAGLLARQMKDQGLKAPIV 245 Query: 251 GPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKN----KALIDAFKAKNQDPSGIFVLP 306 + + +E AI GDA E + T F DP+ KA+++ F+ +P G + L Sbjct: 246 SGDALVTNEYWAITGDAGEDTMMT----FGPDPREKADAKAVVEKFRKAGYEPEG-YTLY 300 Query: 307 AYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWH 364 Y+A+ + A+ +++A D KV+E LR ++ET G +GFD KGD+ + + Y+WH Sbjct: 301 TYAALQIWAEAVKQAKSTDAAKVSEVLRKGSYETVIGKIGFDAKGDVTSPAYVWYKWH 358 Lambda K H 0.316 0.133 0.377 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: 394 Number of extensions: 18 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: 373 Length of database: 366 Length adjustment: 30 Effective length of query: 343 Effective length of database: 336 Effective search space: 115248 Effective search space used: 115248 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 (21.6 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