Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate RR42_RS16970 RR42_RS16970 ABC transporter ATP-binding protein
Query= uniprot:D8IUY5 (404 letters) >FitnessBrowser__Cup4G11:RR42_RS16970 Length = 386 Score = 454 bits (1168), Expect = e-132 Identities = 230/383 (60%), Positives = 284/383 (74%), Gaps = 23/383 (6%) Query: 8 MKRNPQQARISLLLLLALMIVFPFVAQQFG-NSWVRIMDVALLYIMLALGLNVVVGFAGL 66 + + P + +LL L + + PF+ Q G N WVR++D AL+YIMLALGLN+VVGFAGL Sbjct: 15 LTKTPAKTMAALLGFLIIALCAPFLVQTLGGNYWVRVLDFALIYIMLALGLNIVVGFAGL 74 Query: 67 LDLGYIAFYAIGAYSAGLLASPQFAAVIESFVNTYPSVGNFLVWLCGPEIVQNGIHLSLW 126 LDLGYIAFYA+GAY LL SP A E +P NG+HLS+W Sbjct: 75 LDLGYIAFYAVGAYMMALLGSPHLANQFEWIHQLFP----------------NGLHLSMW 118 Query: 127 LIVPISAFLAALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGI 186 ++P++ +AA FG LLGAPTLKLRGDYLAIVTLGFGEIIRIF+NNL+ P+NITNGP+GI Sbjct: 119 FVLPLAVLVAATFGVLLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDRPLNITNGPKGI 178 Query: 187 NLIDPIKVFGVSLAGEPGSGSMVKVFGMSMPSVNAYYFLFLLLCIGVIFFSVRLQDSRLG 246 +DP+ +FG + ++FG+ V YY+L ++L I ++F +RLQ+SR+G Sbjct: 179 TAVDPVHIFGFDFSKSH------EIFGLKFTPVFMYYYLLVVLVIAIVFICLRLQNSRIG 232 Query: 247 RAWVAIREDEIAAKAMGINTRNVKLLAFAMGASFGGVAGAMFGAFQGFVSPESFSLTESI 306 RA+VAIREDEIAAKAMGINTRN+KLLAFAMGASFGG +GA+FGAFQGFVSPESF L ESI Sbjct: 233 RAFVAIREDEIAAKAMGINTRNIKLLAFAMGASFGGASGAVFGAFQGFVSPESFVLWESI 292 Query: 307 AVLAMVVLGGIGHIPGVVLGGVILAALPEVLRHVVEPVQMAIFGKVWIDAEVLRQLLYGL 366 +LA+VVLGG+GHIPGV+LGG++L E+LR V EP Q IFG +DAEVLRQLL+GL Sbjct: 293 YILAIVVLGGMGHIPGVILGGILLVGFQELLRAVAEPAQNMIFGHTIVDAEVLRQLLFGL 352 Query: 367 AMVVIMLTRPAGLWPSPRHEDRP 389 A+V +ML RPAGLWPSPR EDRP Sbjct: 353 ALVGVMLYRPAGLWPSPRKEDRP 375 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: 531 Number of extensions: 21 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: 386 Length adjustment: 31 Effective length of query: 373 Effective length of database: 355 Effective search space: 132415 Effective search space used: 132415 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 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