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 AZOBR_RS31025 AZOBR_RS31025 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__azobra:AZOBR_RS31025 Length = 335 Score = 205 bits (522), Expect = 1e-57 Identities = 122/306 (39%), Positives = 169/306 (55%), Gaps = 16/306 (5%) Query: 21 SVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNG-EFV 79 +V+AV G+ I E EV+G+VGESGCGK+TL ++ ++ P LR G + Sbjct: 38 AVQAVSGVDLSIAEGEVVGLVGESGCGKSTLGRMV-AGILPPSAGT-----LRWRGRDLR 91 Query: 80 ELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHG-IDEEELLDKAR 138 ELS R K I ++ Q M +L P +R+ V HG + E D Sbjct: 92 ELSPADRHHANLK-----IQMVFQDPMASLNPRLRVADIVGEAPVVHGLVPRREAEDYVA 146 Query: 139 RRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLK 198 +VGLDP +++RYP + SGG RQR IA A + P +L+ DE +ALDV Q ++ Sbjct: 147 ATLRQVGLDPAYLRRYPHQFSGGQRQRIGIARALAVKPDVLVCDESVAALDVSIQAQIIN 206 Query: 199 VLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGL 258 + M++ R+ + + +FI+HD+ V I+DR IMY G+IVE AP L +KP HPY + L Sbjct: 207 LFMRL-REELSLTYLFISHDLGVVEHISDRTAIMYLGRIVELAPTPELFDKPNHPYAKAL 265 Query: 259 FNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEPGR 318 + P V+KR I G P+ ++PPSGC FHPRCPHAM C + P L EI P R Sbjct: 266 LDEA--PRVSVEKRRFAPIRGEIPSPLDPPSGCAFHPRCPHAMPRCSAERPALREIAPRR 323 Query: 319 RVACWL 324 AC L Sbjct: 324 WSACHL 329 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: 314 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