Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_011885760.1 ABC transporter ATP-binding protein
Query= uniprot:D8IUY5 (404 letters) >NCBI__GCF_000016205.1:WP_011885760.1 Length = 389 Score = 443 bits (1139), Expect = e-129 Identities = 232/381 (60%), Positives = 281/381 (73%), Gaps = 23/381 (6%) Query: 9 KRNPQQARISLLLLLALMIVFPFV-AQQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLL 67 +RN + + +L A +I P + GN WVR++D A+LY+MLALGLNVVVGFAGLL Sbjct: 16 ERNTTKTVLIGILTAAFVIAAPIIIGSAGGNYWVRVLDFAMLYVMLALGLNVVVGFAGLL 75 Query: 68 DLGYIAFYAIGAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLWL 127 DLGYIAFYA+GAY+A LL+SP + E W+ + NG+H+ + Sbjct: 76 DLGYIAFYAVGAYTAALLSSPHLTSQFE--------------WIAA--LAPNGLHIPFLI 119 Query: 128 IVPISAFLAALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGIN 187 IVPI+ LAA FG LLGAPTL+LRGDYLAIVTLGFGEI+RIFMNNL+ PVNITNGP+GI Sbjct: 120 IVPIAMALAATFGILLGAPTLRLRGDYLAIVTLGFGEIVRIFMNNLDRPVNITNGPKGIT 179 Query: 188 LIDPIKVFGVSLAGEPGSGSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRLQDSRLGR 247 IDP+ + G +L+ +FG +PSV YY+LF+L + VI+ RLQ SR+GR Sbjct: 180 GIDPVHIGGFNLS------QTHSLFGFQLPSVYMYYYLFVLCSLLVIWVCTRLQHSRIGR 233 Query: 248 AWVAIREDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESIA 307 AW AIREDEIAAKAMGINTRNVKLLAFAMGASFGG++GAMFGAFQGFVSPESF+ ESI Sbjct: 234 AWAAIREDEIAAKAMGINTRNVKLLAFAMGASFGGLSGAMFGAFQGFVSPESFTFWESIV 293 Query: 308 VLAMVVLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQLLYGLA 367 VLA VVLGG+GHIPGV+LG V+LA PE LR + P+Q A+FG +D EV+RQ LYGLA Sbjct: 294 VLACVVLGGMGHIPGVILGAVLLAIFPEFLRSTMSPLQHALFGHDIVDTEVIRQALYGLA 353 Query: 368 MVVIMLTRPAGLWPSPRHEDR 388 MVVIML R GLWP+P+HED+ Sbjct: 354 MVVIMLYRSEGLWPAPKHEDK 374 Lambda K H 0.327 0.143 0.430 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: 504 Number of extensions: 17 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: 404 Length of database: 389 Length adjustment: 31 Effective length of query: 373 Effective length of database: 358 Effective search space: 133534 Effective search space used: 133534 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 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