Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate WP_023434291.1 N177_RS20180 branched-chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000496075.1:WP_023434291.1 Length = 369 Score = 288 bits (736), Expect = 2e-82 Identities = 152/355 (42%), Positives = 217/355 (61%), Gaps = 3/355 (0%) Query: 11 LFAAMAIAGFASYSMAA-DTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGA 69 L A + + G A+ AA I IA AGP+TG A +G +AGA A++ IN AGGV G Sbjct: 5 LLAGVVLVGLAAAPGAALAEIAIATAGPMTGQYATFGAQMKAGAEQAVKDINAAGGVLGE 64 Query: 70 QLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSAT 129 QL I DDACDPKQAVAVAN+ V FV GH CS S+ PA+ +Y +EG++ I+P++T Sbjct: 65 QLVLRIGDDACDPKQAVAVANQFAGGDVVFVAGHFCSGSSIPASQVYAEEGIIQISPAST 124 Query: 130 APEIT-SRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188 P T +R IFR G D+ QG VAG+++AE + DK IA++HDK YG+G+A E KK Sbjct: 125 NPTFTENRPGDGIFRVCGRDDQQGQVAGEYLAEHFGDKNIAIVHDKTAYGKGLADETKKY 184 Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDAR 248 + +AG + ++E AG+KD+ AL+SKLK++ V +Y GGYH E GL++RQ + G+D Sbjct: 185 LNEAGKEEVIYEAYTAGEKDYTALVSKLKQSNVDVLYVGGYHTEAGLIVRQMRDQGMDTI 244 Query: 249 FMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAY 308 + + + E +I GDA G L T + K +++ F+ +N +P G +VL Y Sbjct: 245 LVSGDALVTDEYWSITGDAGAGTLMTFSPDPRKSEKAAPVVEEFRGQNIEPEG-YVLYTY 303 Query: 309 SAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363 +A+ + +E AG D + V +AL TF+T G L FD+KGD+ + YEW Sbjct: 304 AAIQAWVQAVEAAGSTDYDAVVDALNEGTFDTVLGELEFDDKGDVTLPGYVFYEW 358 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: 389 Number of extensions: 15 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: 369 Length adjustment: 30 Effective length of query: 343 Effective length of database: 339 Effective search space: 116277 Effective search space used: 116277 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