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 6936572 Sama_0760 iron-compound ABC transporter, ATP-binding protein, putative (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__SB2B:6936572 Length = 271 Score = 77.0 bits (188), Expect = 5e-19 Identities = 72/232 (31%), Positives = 115/232 (49%), Gaps = 26/232 (11%) Query: 25 VDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSSM 84 +DG+SF + + + GV+G +G GK++L ++ ++P + G I L NG+ + L S Sbjct: 20 LDGVSFALSGNGMYGVIGPNGAGKSSLLRCLY-RFIRPDS---GTILL--NGQDIHLYS- 72 Query: 85 TRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHG-IDEEELLDKAR--RRF 141 R+ + + + ++PQ + AL L G + + DK Sbjct: 73 ------RRSFARAVAVVPQE-LPALFDLSTEAVVAMGLIPHKGWLAADSAADKVNIAAAL 125 Query: 142 EEVGLDPLWIKRYPF-ELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVL 200 EVGL+ R PF +LSGG +QRA+IA A + P LI DEPTS LDV + ++VL Sbjct: 126 AEVGLEGYG--RQPFGKLSGGEKQRALIARALVQKPQFLILDEPTSHLDV---RFQIEVL 180 Query: 201 MQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI-VEFAPVESLLEKPL 251 +KR I +I HD+ + D +++M G++ +P E L E L Sbjct: 181 ELLKRLDI--CVICTIHDLNLASALCDELLLMSRGRLEASGSPAEVLTETML 230 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: 215 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: 330 Length of database: 271 Length adjustment: 27 Effective length of query: 303 Effective length of database: 244 Effective search space: 73932 Effective search space used: 73932 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 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