Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate SMa1371 SMa1371 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Smeli:SMa1371 Length = 326 Score = 196 bits (497), Expect = 9e-55 Identities = 113/304 (37%), Positives = 169/304 (55%), Gaps = 10/304 (3%) Query: 5 LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64 LL+ +N+ + +V+A+ G+S + E +G+VGESG GK+ + + + P Sbjct: 3 LLEIDNLHVCFDTRAGTVQALRGVSLTVAPGETLGIVGESGSGKSVTAQAVMGLIDVPGR 62 Query: 65 LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAE 124 + DG+I E L+ R WG+EIT+I Q M +L P + + + + E Sbjct: 63 ISDGEILW----EGKPLAGFAVANAARDIWGREITMIFQNPMTSLNPLMTVGAQIAEVIE 118 Query: 125 SH-GIDEEELLDKARRRFEEVGLDPLW--IKRYPFELSGGMRQRAVIAIATILNPSLLIA 181 H G +A VG+ + +YP E SGGMRQR +IA+ P LLIA Sbjct: 119 VHMGSSRRAARRRAAELLSAVGISGAERRLDQYPHEFSGGMRQRVMIAMGIACEPKLLIA 178 Query: 182 DEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFA 241 DEPT+ALDV Q +L++L +++ + + +I+ ITHD+ V + R+ +MYAG+IVE Sbjct: 179 DEPTTALDVTIQAQILELLAELQEK-MGLAIVLITHDLGIVAGLCHRVAVMYAGQIVETG 237 Query: 242 PVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAM 301 PV+++ E P HPYTQGL S TP + + +T I GAPP L+ PPSGC F PRCP Sbjct: 238 PVDAIFENPSHPYTQGLIRS--TPGLDADEERLTAIDGAPPGLLQPPSGCAFLPRCPIGD 295 Query: 302 DVCK 305 + C+ Sbjct: 296 EGCQ 299 Lambda K H 0.321 0.138 0.405 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: 276 Number of extensions: 11 Number of successful extensions: 5 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: 330 Length of database: 326 Length adjustment: 28 Effective length of query: 302 Effective length of database: 298 Effective search space: 89996 Effective search space used: 89996 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: 49 (23.5 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