Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_101443030.1 BD749_RS03795 ATP-binding cassette domain-containing protein
Query= SwissProt::P9WQI3 (393 letters) >NCBI__GCF_002846395.1:WP_101443030.1 Length = 259 Score = 132 bits (331), Expect = 1e-35 Identities = 73/220 (33%), Positives = 122/220 (55%), Gaps = 13/220 (5%) Query: 15 DGHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGELRIAGERVNEKAPK 74 D ++ ++L + GE L+++G SG GK+ + +I+GL G + + G V P+ Sbjct: 27 DDFEVLKGVDLDLFKGENLVVLGRSGTGKSVLIKIISGLLQADEGSVNVLGREVGALKPR 86 Query: 75 DRD-----IAMVFQSYALYPHMTVRQNIAFPLT-----LAKMRKADIAQKVSETAKILDL 124 + D I FQ+ ALY MTVR+N+ FPL + + + D Q V E +L Sbjct: 87 ELDALRLKIGFSFQNSALYDSMTVRENLEFPLIRHAKHMTEAEREDTIQYVLEAVGLLQA 146 Query: 125 TNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQLQRRL 184 N + PS+LSGGQR+R+ + R ++ P L DEP + LD +++ I ++Q + Sbjct: 147 INQM---PSELSGGQRKRIGIARTLILKPDIMLYDEPTAGLDPITCIEINSLINEVQEKF 203 Query: 185 GTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYE 224 T+++ +THD T A +GDR+V++ G Q+ GT +E++E Sbjct: 204 NTSSIIITHDLTCARAVGDRIVMLLDGQFQREGTFDEVFE 243 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: 194 Number of extensions: 11 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: 393 Length of database: 259 Length adjustment: 27 Effective length of query: 366 Effective length of database: 232 Effective search space: 84912 Effective search space used: 84912 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: 48 (23.1 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