Align ABC-type branched-chain amino acid transport system, periplasmic component protein (characterized, see rationale)
to candidate Dsui_2061 Dsui_2061 ABC-type branched-chain amino acid transport system, periplasmic component
Query= uniprot:D8IUY1 (378 letters) >FitnessBrowser__PS:Dsui_2061 Length = 384 Score = 121 bits (304), Expect = 3e-32 Identities = 109/356 (30%), Positives = 162/356 (45%), Gaps = 19/356 (5%) Query: 8 LNIIAASLALIPAFAMAQETQV--VKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPI 65 + + SL L+ A A A Q +KIG ++ LTG A G + G +A + +NA+ Sbjct: 1 MRFLPKSLVLVGALAAAGLAQAADIKIGVAAALTGGAAQYGVAIRNGFQLAADEINAKG- 59 Query: 66 TVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQG-VKAIVGPYNSGVTIPASRVYNDAGI 124 V G KI+ ++ ED+Q + G+ V +KL Q V + GP S A V N A Sbjct: 60 GVNGNKIQ--LVVEDEQGKKEEGINVFKKLIFQDKVLMVFGPTLSNSMFAAGPVANGAKT 117 Query: 125 VV-ATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVI---DDRTAYG 180 VV T + IT G +FR + +S + A K K K+VAVI DD A+ Sbjct: 118 VVFGTSVTANGITDIG-PYVFRNSVMESDVLPVTVATATKHYKLKQVAVIYGNDD--AFT 174 Query: 181 QGLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKR 240 + F KV + + V +T+ DF A LT IK PDAV A + I Sbjct: 175 KSGYDVFKKVLEDQKLPVTTTETYVKGDVDFKAQLTKIKASNPDAVICSCLAEEAANIML 234 Query: 241 QMKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKY 300 Q + LG+ VP +GG+G SP++ + A GE + + + A K F Y KKY Sbjct: 235 QARGLGIKVPFIGGNGFNSPKLFEISKLA-GEGTFVGSPWSNTNPAPANKAFVAAYVKKY 293 Query: 301 NRPAETYAVSFYDGMMLIAQAMKQAN-----SVDPKQFGPALAKISYKGVAGQYDF 351 N +A +D + + A A+++ + D + AL K + G G + F Sbjct: 294 NAEPNQFAAQAFDALHVAAAALQEVKLSGDIAADREALKNALPKATINGATGPFKF 349 Lambda K H 0.316 0.134 0.378 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: 423 Number of extensions: 23 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: 378 Length of database: 384 Length adjustment: 30 Effective length of query: 348 Effective length of database: 354 Effective search space: 123192 Effective search space used: 123192 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