Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 206137 DVU0712 amino acid ABC transporter, periplasmic-binding protein
Query= SwissProt::P21175 (373 letters) >MicrobesOnline__882:206137 Length = 376 Score = 204 bits (518), Expect = 4e-57 Identities = 121/366 (33%), Positives = 197/366 (53%), Gaps = 8/366 (2%) Query: 3 KGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINK 62 KG RL + ++ A+ + AA +++ L P+TG A G R + E++NK Sbjct: 2 KGVVRLLAVCMVTSLL-MAATAFAAGPVRVGLMCPLTGKWASEGQDMRNIVELLAEEVNK 60 Query: 63 AGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVL 122 AGG+NG ++E ++ DD DP+ A A K+ GV V+G S+ T+ + +IY++ G+ Sbjct: 61 AGGINGNKVELIVEDDGGDPRTAALAAQKLSTSGVTAVIGTYGSAVTEASQNIYDEAGIA 120 Query: 123 MITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIA 182 I +T +T +G KL RT D+ QG VA K I + K +A+LHD Y +G+A Sbjct: 121 QIATGSTNVRLTEKGLKLFLRTCPRDDEQGRVAAKVIKNK-GYKAVALLHDNSSYAKGLA 179 Query: 183 TEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQ 242 E K ++ G K+ ++ L G++D+ A+++KLK A ++F GY+PE+G+LLRQ + Sbjct: 180 DETKALLDKDGTKIVFYDALTPGERDYTAILTKLKAANPDIIFFTGYYPEVGMLLRQKME 239 Query: 243 AGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQD---PKNKALIDAFKAK-NQD 298 + MG + N ++ IAG A+ L QD + KA + A+KAK N Sbjct: 240 MKWNVPMMGGDAANNLDLVKIAGKAAAKGYFFLSPPVPQDFDTAEAKAFLAAYKAKHNAL 299 Query: 299 PSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETP--TGNLGFDEKGDLKNF 356 P+ ++ + A A VI + ++K G+AD +A L+ P +G + F+EKGD Sbjct: 300 PNSVWSVLAGDAFKVIVEAVQKGGKADGAGIATYLKTQLKNYPGLSGQISFNEKGDRVGD 359 Query: 357 DFTVYE 362 + VY+ Sbjct: 360 LYRVYD 365 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: 347 Number of extensions: 15 Number of successful extensions: 4 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 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