Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate 209225 DVU0291 ABC transporter, ATP-binding protein
Query= SwissProt::P9WQI3 (393 letters) >MicrobesOnline__882:209225 Length = 354 Score = 174 bits (441), Expect = 4e-48 Identities = 116/332 (34%), Positives = 168/332 (50%), Gaps = 19/332 (5%) Query: 16 GHTAVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSGELRIAGERVNEKAPKD 75 G + D+NLT A GE + LVGPSG GKTT L IAGL+ G +R+ + + Sbjct: 14 GREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIRVTPPQGHGGG--- 70 Query: 76 RDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETAKIL-----DLTNLLDR 130 + +VFQ Y L+PH++V +N+AF +R A + ++V + DL ++ R Sbjct: 71 --VVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRLDTDDLAHMASR 128 Query: 131 KPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQLQRRLGTTTVY 190 P+QLS GQRQRVA+ RA+V P L+DEP +NLD LR +M + + RR G TV Sbjct: 129 YPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVVRRFGVATVT 188 Query: 191 VTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPAMNFFPARLTAI 250 VTHD EA +GDR+ VM GG Q+ P ++Y PA+ A F+G + R T Sbjct: 189 VTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLGPVTVLDETTRRTLG 248 Query: 251 GLTLPFGEVTLAPEVQGVIAAHPKPENVIVGVRPEHIQDAALIDAYQRIRALTFQVKVNL 310 T P A +QG+ P+ + VRP A L+ A T QV L Sbjct: 249 IDTPPAAATACADTMQGLRLYRPE----ALAVRPWADGPAVLVSA-----RFTGQVMQLL 299 Query: 311 VESLGADKYLYFTTESPAVHSVQLDELAEVEG 342 ++ G + ++ ++P + L E+ G Sbjct: 300 LDVEGQELLVHTLDDAPPTGTRLCVSLREIPG 331 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: 347 Number of extensions: 18 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: 354 Length adjustment: 30 Effective length of query: 363 Effective length of database: 324 Effective search space: 117612 Effective search space used: 117612 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