Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate AO353_13340 AO353_13340 amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13340 Length = 377 Score = 280 bits (715), Expect = 6e-80 Identities = 152/358 (42%), Positives = 217/358 (60%), Gaps = 9/358 (2%) Query: 12 FAAMAIA---GFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNG 68 F A+A+A G +S+ A +K+ +AGP+TGP A +G GA A + IN GG+NG Sbjct: 10 FVALAVAAALGVSSFVQA--DVKLGVAGPMTGPSASFGLQYMKGAQAAADAINAKGGING 67 Query: 69 AQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSA 128 ++ V DDAC+PKQAVAVANK+V D V VVGH CSSST PA+++Y D G++ ITP + Sbjct: 68 EKIVLVQGDDACEPKQAVAVANKMVQDKVIGVVGHFCSSSTIPASEVYSDAGIIAITPGS 127 Query: 129 TAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188 T P +T RG + R G D+ QG VAG +I + K K +AV++DK YG+G+A K Sbjct: 128 TNPTVTERGLPAMMRMCGRDDQQGIVAGNYIVDVLKGKKVAVINDKDTYGKGLADATAKQ 187 Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGL-DA 247 + G+K + EGL G+KDF+ALI+K++ G +YFGG HPE G L+ Q ++ GL D Sbjct: 188 LTARGVKPVLEEGLTRGEKDFSALITKVRSVGADVLYFGGLHPEAGPLVHQLREQGLKDV 247 Query: 248 RFMGPEGVGNSEITAIAGDAS--EGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVL 305 +FM +G+ E+ AG A +G+ T P +KA++D F+ +P G + L Sbjct: 248 KFMSDDGIVTDEMVTTAGGAPYVDGVYMTFGADPRLIPDSKAVVDTFRKSGYEPEG-YTL 306 Query: 306 PAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363 AY++V +A G A E+ A+ L+A+ ET G +D KGDLK D+ VY+W Sbjct: 307 YAYASVQALAAGFNGAKSNKGEEAAKWLKAHPVETVMGKKEWDSKGDLKISDYVVYQW 364 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: 396 Number of extensions: 27 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: 377 Length adjustment: 30 Effective length of query: 343 Effective length of database: 347 Effective search space: 119021 Effective search space used: 119021 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