Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_008507466.1 BIBO1_RS12220 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000182725.1:WP_008507466.1 Length = 371 Score = 288 bits (737), Expect = 2e-82 Identities = 148/337 (43%), Positives = 208/337 (61%), Gaps = 2/337 (0%) Query: 30 IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQLEGVIYDDACDPKQAVAVA 89 I + + P+TG A +G+ + G A+ + N GG+NG Q+ V DDA DPKQ ++VA Sbjct: 25 IMVGVGAPLTGSQAAFGEQIKRGVEAAVAEANAKGGMNGEQITLVYGDDAADPKQGISVA 84 Query: 90 NKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTIGLDN 149 NK V DGVKFV+GH S + P +DIY + GVLMI P T P T R FRT D+ Sbjct: 85 NKFVGDGVKFVIGHFNSGVSIPTSDIYAENGVLMIAPGTTNPTFTERELWNTFRTCRRDD 144 Query: 150 MQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAGDKDF 209 QG VAGK++A+ YKD +A+LHDK YG+G+A E KK++ + G+K ++EG+N GDKDF Sbjct: 145 KQGIVAGKYMADNYKDGKVAILHDKTPYGQGLADETKKSLNENGMKETLYEGVNQGDKDF 204 Query: 210 NALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAGDASE 269 +ALISK+K AG+ VY+GG HPE GLL+RQ GL A+F+ +G+ ++E+ +IAGDA Sbjct: 205 SALISKMKAAGITAVYWGGMHPEAGLLIRQMADQGLKAQFISGDGIVSNELASIAGDAVA 264 Query: 270 GMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEADPEKV 329 G++ T D N LI AF+ K +P + AY+ V + AG DP +V Sbjct: 265 GVMNTFGPDPRDDKANAELIKAFRDKGFEPEA-YTFYAYAGVQSLVNAANAAGSNDPMEV 323 Query: 330 AEALR-ANTFETPTGNLGFDEKGDLKNFDFTVYEWHK 365 A A++ F+T G++ FD KGD + ++EW K Sbjct: 324 ATAMKEKGPFKTVLGDISFDAKGDPSLSPYVMFEWRK 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: 434 Number of extensions: 17 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: 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 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