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 HSERO_RS07885 HSERO_RS07885 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__HerbieS:HSERO_RS07885 Length = 335 Score = 206 bits (525), Expect = 5e-58 Identities = 119/301 (39%), Positives = 177/301 (58%), Gaps = 13/301 (4%) Query: 24 AVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVELSS 83 A+D + ++L EV+G+VGESGCGK+TL V ++ P DG++ VNG S Sbjct: 44 ALDKVDLKVLPGEVVGLVGESGCGKSTLGRVA-CGLLDPS---DGQVL--VNGRD-RASL 96 Query: 84 MTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEEELLDKARRRFEE 143 +R+E + + + I P A++N P +R+++ V A+ +G E +L D ++ Sbjct: 97 SSREEAEARLQVQMIFQNPYASLN---PRLRIDQIVGEAAQVNGKVEGDLDDYVCQQLLR 153 Query: 144 VGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVLMQM 203 GLDP RYP + SGG RQR IA A + P +L+ DE +ALDV Q +L + M + Sbjct: 154 AGLDPALRDRYPHQFSGGQRQRIGIARALAVQPQMLVCDEAVAALDVSIQAQILNLFMDL 213 Query: 204 KRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGLFNSVL 263 + + + + +FI+HD+ V ++DR++IMY G++VE APV L +P HPYTQ L V Sbjct: 214 RAE-LGLTYLFISHDLGVVEHVSDRVVIMYLGRVVESAPVAELFGQPNHPYTQALLAEV- 271 Query: 264 TPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEPGRRVACW 323 P +K+ T I G P+ +NPP+GC F+PRCPHA C+E++P L EI PG AC Sbjct: 272 -PRMGARKKEFTAIKGEIPSPLNPPTGCHFNPRCPHATQRCREEQPLLREIAPGHMSACH 330 Query: 324 L 324 L Sbjct: 331 L 331 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: 316 Number of extensions: 15 Number of successful extensions: 4 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: 335 Length adjustment: 28 Effective length of query: 302 Effective length of database: 307 Effective search space: 92714 Effective search space used: 92714 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