Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_011767451.1 AZO_RS18710 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000061505.1:WP_011767451.1 Length = 374 Score = 207 bits (526), Expect = 5e-58 Identities = 121/352 (34%), Positives = 192/352 (54%), Gaps = 10/352 (2%) Query: 11 LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70 L A +A+ G S ++A +KI AGP+TGP+A +G GA +A+E N G G Q Sbjct: 9 LAATLALVG-NSAALAQTVVKIGHAGPLTGPIAHFGKDGEMGARLAVEDANARGITLGGQ 67 Query: 71 ---LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPS 127 E V DD DP+ A VA ++ + GVK VVGHV S ++ PA+ +YE GV ++TPS Sbjct: 68 KVKFELVSEDDQGDPRTATTVAQRLTDLGVKGVVGHVTSGASIPASRVYEQAGVPVVTPS 127 Query: 128 ATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKK 187 +T+P++T +GYK+ FR I D QG K+ AE K +A++ D+ YG+G+A Sbjct: 128 STSPKLTRQGYKVTFRVIANDLQQGEATAKYAAETLKAAKVAIIDDRTAYGQGLADAFAD 187 Query: 188 TVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDA 247 + G++V E DF A+++K+K V++GG + +LRQ +Q G A Sbjct: 188 AAKQRGLQVVGREFTTDKSTDFLAILTKIKAKAPDAVFYGGMDAQAAPMLRQLRQLGSSA 247 Query: 248 RFMGPEGVGNSEITAIAGDASEGML----ATLPRAFEQDPKNKALIDAFKAKNQDPSGIF 303 ++G +GV E+ +AGDA + A+LP A + P + FK + + ++ Sbjct: 248 IYLGGDGVCTGEMIKLAGDAMSDKVYCSQASLPPA--KMPGGTDFLSRFKQRYKADVLLY 305 Query: 304 VLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKN 355 +Y A T + + ++ A ++P K AL+ F+ TG + FD +GD++N Sbjct: 306 APYSYDAATALIEAMKAADSSEPAKYLPALQRVAFKGVTGEIAFDPQGDIRN 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: 352 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: 373 Length of database: 374 Length adjustment: 30 Effective length of query: 343 Effective length of database: 344 Effective search space: 117992 Effective search space used: 117992 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: 50 (23.9 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