Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate RR42_RS14425 RR42_RS14425 leucine ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Cup4G11:RR42_RS14425 Length = 371 Score = 434 bits (1117), Expect = e-126 Identities = 214/365 (58%), Positives = 275/365 (75%), Gaps = 2/365 (0%) Query: 7 RLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGV 66 RL+ + A A+ + + A+TIKIA+AGP++G VAQYGDM +AGAL AIEQIN AGG Sbjct: 5 RLTSISLATALCALGA-AANAETIKIAIAGPMSGSVAQYGDMVKAGALTAIEQINAAGGA 63 Query: 67 NGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITP 126 G + E V+ DDAC+PKQAVAVANK+V+ + +V+GHVCS ST PA+DIYE+EG++M+TP Sbjct: 64 GGNKFEVVMMDDACEPKQAVAVANKIVSQKIHYVIGHVCSGSTIPASDIYENEGIVMVTP 123 Query: 127 SATAPEIT-SRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEV 185 SATAP++T ++ K IFRTIG D+ QGP A ++I + K K +A+LHDKQ YG+GIA+ V Sbjct: 124 SATAPQLTENKKRKFIFRTIGRDDQQGPAAAQYIITKIKPKKVAILHDKQSYGQGIASSV 183 Query: 186 KKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGL 245 KK +E A I VAVFEG+NAGD D++A+I+KLK GV FVYFGGYHPEMGLLLRQA++ G+ Sbjct: 184 KKDLEAAKIPVAVFEGVNAGDSDYSAVITKLKSQGVDFVYFGGYHPEMGLLLRQAREQGV 243 Query: 246 DARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVL 305 A FMGPEGVGN ++TAIAG +SEGML TLP F DP N AL+ AF K +D +G F + Sbjct: 244 KATFMGPEGVGNKDVTAIAGASSEGMLVTLPADFSADPSNAALVKAFADKKRDANGPFQM 303 Query: 306 PAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHK 365 PAY+AV +I I A DP KVA + N F+TP G + +D +GDLK+F F V+ WHK Sbjct: 304 PAYAAVQIIGDAIAGAKSTDPTKVAAYMHKNAFQTPIGKVEYDAQGDLKSFKFVVFTWHK 363 Query: 366 DATRT 370 DAT+T Sbjct: 364 DATKT 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: 462 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: 371 Length adjustment: 30 Effective length of query: 343 Effective length of database: 341 Effective search space: 116963 Effective search space used: 116963 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