Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_011385357.1 AMB_RS15010 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000009985.1:WP_011385357.1 Length = 366 Score = 289 bits (739), Expect = 1e-82 Identities = 149/353 (42%), Positives = 220/353 (62%), Gaps = 6/353 (1%) Query: 11 LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70 L AA+ +AG A AD I I +AGP++G A +G+ + GA+ A+E IN GGV G + Sbjct: 11 LAAALLMAGAAR----AD-ITIGVAGPLSGSEAAFGEQFKRGAMKAVEDINAKGGVLGQK 65 Query: 71 LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130 L + DDACDPKQAVAVAN++ V FV GH CS S+ PA+++Y + G+L I+P++T Sbjct: 66 LALTLGDDACDPKQAVAVANEMAAKKVPFVAGHFCSGSSIPASEVYAETGILQISPASTN 125 Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190 P+ T RG IFRT G D+ QG +A +IA+ KDK +A++HDK YG+G+A + + + Sbjct: 126 PKFTERGLPNIFRTCGRDDQQGVIAADYIAKHQKDKVVAIVHDKSAYGKGLADQTRDALG 185 Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250 AGIK A++E ++AG+KD++AL++KLK + V +YFGGY E GL++RQ + G+ R M Sbjct: 186 KAGIKAALYEAISAGEKDYSALVTKLKASKVDLLYFGGYKTEAGLIVRQLRDQGMQTRLM 245 Query: 251 GPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSA 310 G + + E AI G A EG + T ++P N L+ ++A+ +P + L Y Sbjct: 246 GGDALVTEEYWAITGAAGEGTMMTFSPDPRKNPANADLVKYYRAQKYEPEA-YTLYTYGT 304 Query: 311 VTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363 + A+ EKA D +KVA L+A F+T G +GFD KGD+ + +Y W Sbjct: 305 IQAWAQAAEKAKTTDWKKVAAVLKAEKFDTAIGKIGFDAKGDVAAPGYVMYVW 357 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: 339 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 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