Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= SwissProt::P9WQI3 (393 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 232 bits (591), Expect = 1e-65 Identities = 138/296 (46%), Positives = 184/296 (62%), Gaps = 9/296 (3%) Query: 4 IVLDHVNKSYPDGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGELRI 63 I L H K++ DG A++ L+L I GE ++L+GPSGCGKTTTL +IAGLE +G + + Sbjct: 7 ITLRHCGKTFADGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVM 66 Query: 64 AGERVNEKAP-KDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAKIL 122 G+ P + R + MVFQSYAL+P+MTV +NIA+ L + ++ A ++V E ++ Sbjct: 67 FGDNDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMM 126 Query: 123 DLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQLQR 182 L +R+ QLSGGQRQRVA+ RAI P+ L+DEPL+ LDAKLR +R +I QL R Sbjct: 127 HLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLR 186 Query: 183 RLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAMNF 242 L T VYVTHDQ EAM LGDR++VM G Q GTP+++Y PAN FVA FIG+ MN Sbjct: 187 SLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--MNR 244 Query: 243 FPARLTAIGLTLPFGEVTLAPE--VQGVIAAHPKPENVIVGVRPEHIQDAALIDAY 296 PA L A +P G L P +AA P P ++ RPE + A DA+ Sbjct: 245 LPAVLEADAWRVPGG---LVPRHGTAASLAAAPSPRAELL-FRPEDVALAQAEDAH 296 Lambda K H 0.319 0.135 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: 373 Number of extensions: 18 Number of successful extensions: 2 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: 393 Length of database: 357 Length adjustment: 30 Effective length of query: 363 Effective length of database: 327 Effective search space: 118701 Effective search space used: 118701 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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