Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate Dsui_0630 Dsui_0630 ABC-type branched-chain amino acid transport system, periplasmic component
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__PS:Dsui_0630 Length = 434 Score = 209 bits (531), Expect = 2e-58 Identities = 118/339 (34%), Positives = 181/339 (53%), Gaps = 4/339 (1%) Query: 29 TIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG-GVNGAQL--EGVIYDDACDPKQA 85 T+KI A P+TGP A G GA +AIE++N G + GA++ E + DD DPKQ Sbjct: 45 TVKIGHASPLTGPQAHIGKDNEYGATLAIEELNAKGLEIGGAKVKFELISDDDQADPKQG 104 Query: 86 VAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATAPEITSRGYKLIFRTI 145 VA K V+ V V+GH+ S +T PA+ IY D G+ I+ SAT P T +G+ FR + Sbjct: 105 TTVAQKFVDAKVNGVIGHLNSGTTIPASKIYFDAGIPQISGSATNPTYTKQGFATAFRVM 164 Query: 146 GLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVEDAGIKVAVFEGLNAG 205 D QG +F A+ K++A++ D+ YG+G+A E KK E AG+KV E N Sbjct: 165 ANDEQQGKALAQFAAKTLAAKSVAIIDDRTAYGQGLADEFKKAAEAAGLKVVASEYTNDK 224 Query: 206 DKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDARFMGPEGVGNSEITAIAG 265 DF A+++K+K +++GG P+ G + +Q K+ GL A+F+ +G +AG Sbjct: 225 ATDFKAILTKIKSKKPDLIFYGGMDPQGGPMAKQMKELGLKAKFLTGDGGCTPNFITLAG 284 Query: 266 DASEGMLATLPRA-FEQDPKNKALIDAFKAKNQDPSGIFVLPAYSAVTVIAKGIEKAGEA 324 A+EG +LP ++ P D F K + ++ Y A V+ +++A Sbjct: 285 AAAEGQYCSLPGVPLDKMPGGTVFKDKFVGKFKTEIQLYAPYVYDATMVLVDAMKRANSV 344 Query: 325 DPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363 +P K + +F+ T +GFDE GDLK+ + YE+ Sbjct: 345 EPAKYLPEIGKTSFQGVTAKIGFDEFGDLKDGAISFYEY 383 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: 425 Number of extensions: 27 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: 434 Length adjustment: 31 Effective length of query: 342 Effective length of database: 403 Effective search space: 137826 Effective search space used: 137826 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