Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate SMc01946 SMc01946 leucine-specific binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Smeli:SMc01946 Length = 372 Score = 331 bits (849), Expect = 2e-95 Identities = 168/357 (47%), Positives = 237/357 (66%), Gaps = 3/357 (0%) Query: 11 LFAAMAIAGFASYSMAA-DTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGA 69 L +A+A+ ++S A I + + GP+TGP A +G + GA A E IN AGG+NG Sbjct: 5 LLSAVALTAMVAFSGTAWADILVGVGGPLTGPNAAFGAQLQKGAEQAAEDINAAGGINGE 64 Query: 70 QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129 Q++ V+ DD DPKQ V+VA K V DGVKFVVGH S + PA++IY + G+L +TP++T Sbjct: 65 QIKVVLGDDVSDPKQGVSVAQKFVADGVKFVVGHFNSGVSIPASEIYAENGILQVTPAST 124 Query: 130 APEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTV 189 P+ T RG FRT G D+ QG VAG +IA +KD +AV+HDK YG+G+A E KK++ Sbjct: 125 NPQFTERGLWNTFRTCGRDDQQGAVAGAYIAANFKDAKVAVIHDKTPYGQGLADETKKSM 184 Query: 190 EDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARF 249 +AG+ A++EG+N GDKDF+ALI+K+K+AGV VY+GG H E GL++RQ K GL A Sbjct: 185 NEAGVTEALYEGINTGDKDFSALIAKMKQAGVSIVYYGGLHTEAGLIMRQMKDQGLKATM 244 Query: 250 MGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYS 309 M +G+ ++E+ +IAGDA +G L T + P K L++ F+A +P + L AY+ Sbjct: 245 MSGDGIVSNELASIAGDAVDGTLMTFAPDPRKSPAAKDLVEKFRAAGFEPEA-YTLYAYA 303 Query: 310 AVTVIAKGIEKAGEADPEKVAEALRA-NTFETPTGNLGFDEKGDLKNFDFTVYEWHK 365 A+ VIA+G + AG DP+ VAEA++A F+T G LGFDEKGD+ D+ +Y W K Sbjct: 304 ALQVIAEGAKAAGNTDPQAVAEAIKAKGPFKTAIGELGFDEKGDITRPDYVMYTWKK 360 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: 427 Number of extensions: 12 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: 372 Length adjustment: 30 Effective length of query: 343 Effective length of database: 342 Effective search space: 117306 Effective search space used: 117306 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 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