Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate YP_426833.1 Rru_A1746 extracellular ligand-binding receptor
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000013085.1:YP_426833.1 Length = 368 Score = 303 bits (777), Expect = 4e-87 Identities = 152/353 (43%), Positives = 226/353 (64%), Gaps = 2/353 (0%) Query: 11 LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70 L AA A S AD I + +AGP+TG A +G+ GA A++ IN GGV G + Sbjct: 8 LLAATAAFAMGVGSAQAD-ITVGVAGPMTGQYASFGEQLAKGAEQAVKDINAKGGVLGEK 66 Query: 71 LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130 L DDACDPKQAVAVAN+ VND V FV GH CS S+ PA+ +Y +EG++ I+P++T Sbjct: 67 LVLKKGDDACDPKQAVAVANQFVNDKVVFVAGHFCSGSSIPASAVYNEEGIVQISPASTN 126 Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190 P++T +G++ +FRT G D+ QGP AG F+ + + IA++HDK YG+G+A E K + Sbjct: 127 PKLTEQGFENVFRTCGRDDQQGPTAGDFLKAHFPGQKIAIIHDKTAYGKGLADETKSALN 186 Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250 AG++ A++E + AG+KD++AL++KLK G++ +Y GGYH E GL++RQAK+ GLDAR + Sbjct: 187 KAGVQEALYEAITAGEKDYSALVTKLKNEGIKIIYLGGYHTEAGLIIRQAKEQGLDARIV 246 Query: 251 GPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPAYSA 310 + + +SE +IAG A +G L T ++P+ A++ +F + G + L Y A Sbjct: 247 SGDALVSSEFASIAGPAGDGTLFTFSPDPRKNPEAAAVVKSFTDAGYNAEG-YTLYTYGA 305 Query: 311 VTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363 V A+ +EKA D +KVA+AL++ F T G +GFD +GD+ + +YEW Sbjct: 306 VQAWAQAVEKAKSTDVDKVAKALKSGQFSTVLGPIGFDAQGDVSAPGYVMYEW 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: 458 Number of extensions: 20 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: 368 Length adjustment: 30 Effective length of query: 343 Effective length of database: 338 Effective search space: 115934 Effective search space used: 115934 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