Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate YP_002823734.1 NGR_b15300 amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >NCBI__GCF_000018545.1:YP_002823734.1 Length = 364 Score = 251 bits (642), Expect = 2e-71 Identities = 135/357 (37%), Positives = 204/357 (57%), Gaps = 10/357 (2%) Query: 11 LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70 L A +A + + A+ I I +AGP+TG +A G + GA MA+ +IN AGGV G Q Sbjct: 5 LVLAAILASTLGFPVQAE-ILIGVAGPMTGKLAWTGTQLKRGAEMAVARINAAGGVLGEQ 63 Query: 71 LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130 + ++ DD CD +QAVA A K+V D V+GH CS ++ PA+ IY GV+ I+PS+T Sbjct: 64 IRLIVADDFCDAQQAVAAAQKLVADKAVLVIGHYCSGASIPASKIYAKAGVVQISPSSTN 123 Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190 P +T +GY +FR D+ QG AG ++A+ + DK IA+LHD YG+G+A E +K + Sbjct: 124 PTLTEQGYANVFRVCSRDDAQGLQAGNYLADHWGDKKIAILHDDTTYGKGLAEETRKQLN 183 Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFM 250 G+ +++ G D++A I+ + AG+ +Y GGYH E L++R A++ + + Sbjct: 184 KRGVNETIYQSYEPGKDDYSAEIAGFQTAGIAVLYLGGYHTEAALMVRAARERAYPVQVI 243 Query: 251 GPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKA----LIDAFKAKNQDPSGIFVLP 306 + IAG A+EG L T F DP+ A ++ F+A+N +P + L Sbjct: 244 SGDDTATEAFGLIAGPAAEGTLFT----FVADPRRNAEAADVVARFRAENFEPDS-WTLH 298 Query: 307 AYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363 +Y A V A+ + KAG DP+K+ E LR F+T G + FDEKGDL ++ Y W Sbjct: 299 SYGAAEVWAQAVRKAGSLDPQKITETLRKYQFDTVLGRIDFDEKGDLTVQNWVWYVW 355 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: 330 Number of extensions: 18 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: 364 Length adjustment: 30 Effective length of query: 343 Effective length of database: 334 Effective search space: 114562 Effective search space used: 114562 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