Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_045585665.1 AL072_RS27965 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_001305595.1:WP_045585665.1 Length = 376 Score = 291 bits (746), Expect = 2e-83 Identities = 154/362 (42%), Positives = 227/362 (62%), Gaps = 10/362 (2%) Query: 7 RLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGV 66 R + L +++A + AAD +K+ LAGPVTG A + + R GA +A+ +N AGG+ Sbjct: 13 RSNLLRFGISLAALVPTAAAAD-VKLGLAGPVTGQYASFMEQMRRGADLAVADLNAAGGI 71 Query: 67 NGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITP 126 NG ++ + DDACDPKQAVAVAN+ V DGV+ VVGH CSSST PA+ +Y + G++++TP Sbjct: 72 NGEKVVLQVADDACDPKQAVAVANRFVADGVQAVVGHFCSSSTIPASSVYAESGLVIVTP 131 Query: 127 SATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVK 186 ++T P IT RG +FR G D+ VA K I R +TIA++HDK YG+GIA V+ Sbjct: 132 ASTNPTITERGLTNMFRVCGRDDQAAGVAAKQIVGRNLGRTIAIVHDKSTYGQGIAEGVR 191 Query: 187 KTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLD 246 + G V +FEG+ G++DF++L++++K V V+FGGYH E GLL+RQA + GL Sbjct: 192 TELAQQGRNVVLFEGITQGERDFSSLVARMKALNVDVVFFGGYHTEAGLLVRQASEQGLK 251 Query: 247 ARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKA----LIDAFKAKNQDPSGI 302 RF+ +G+ +E +IAG AS+G++ T F DP+ A L+ F+ +P G Sbjct: 252 TRFVAGDGLATTEFASIAGPASDGVMFT----FYPDPRANAGTADLVRRFRTAGFEPEG- 306 Query: 303 FVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYE 362 F L Y+AV V+A + A +++A+ALRA T+ T G++ FD KGD + F +Y Sbjct: 307 FTLYTYAAVRVLADAAKAAKTMKGDRLADALRAGTYHTVLGDIRFDRKGDPNSEPFVLYA 366 Query: 363 WH 364 W+ Sbjct: 367 WN 368 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: 374 Number of extensions: 16 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: 376 Length adjustment: 30 Effective length of query: 343 Effective length of database: 346 Effective search space: 118678 Effective search space used: 118678 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