Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_088755389.1 CEJ45_RS12295 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_002213425.1:WP_088755389.1 Length = 381 Score = 206 bits (525), Expect = 7e-58 Identities = 127/366 (34%), Positives = 188/366 (51%), Gaps = 10/366 (2%) Query: 13 AAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG---GVNGA 69 A +A FA + A + IKI P+TGP A G GA MA++++N G G Sbjct: 12 ALVAAFSFAGAAQAQEVIKIGHVAPLTGPNAHIGKDNENGARMAVDELNAKGFEIGGKKV 71 Query: 70 QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129 + V DDA DPKQA VA +V+ VK VVGH+ S +T PA+ IY D G+ I+PSAT Sbjct: 72 TFQLVPQDDASDPKQATTVAQALVDAKVKGVVGHMNSGTTIPASKIYYDAGIPQISPSAT 131 Query: 130 APEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTV 189 P+ T +G+ FR + D G V G++ K K +AV+ D+ YG+G+A E +K+ Sbjct: 132 NPKYTQQGFNTAFRVVANDGQLGGVLGRYAVNELKGKNVAVIDDRTAYGQGVAEEFRKSA 191 Query: 190 EDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARF 249 AG + + DFNA+++ +K V+FGG G +LRQ Q G+ A+F Sbjct: 192 LAAGATIVATQYTTDKATDFNAILTSVKSKKPDLVFFGGMDAVAGPMLRQMDQLGVAAKF 251 Query: 250 MGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAK-----NQDPSGIFV 304 MG +G+ +E+ ++AG + A K ++ FKA NQD I+ Sbjct: 252 MGGDGICTTELPSLAGAGLKDSEVVCAEAGGVTEAGKKPLEDFKAAYKKKFNQDVV-IYA 310 Query: 305 LPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWH 364 Y A+ +A +++AG +DP+ L + TG + FD KGD+ N T+Y + Sbjct: 311 PYTYDALMTLADAMKQAGSSDPKVYLPVLAKIKHKGVTGEIAFDAKGDILNGTLTLYT-Y 369 Query: 365 KDATRT 370 K RT Sbjct: 370 KGGKRT 375 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: 369 Number of extensions: 21 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: 381 Length adjustment: 30 Effective length of query: 343 Effective length of database: 351 Effective search space: 120393 Effective search space used: 120393 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