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 H281DRAFT_01031 H281DRAFT_01031 peptide/nickel transport system ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Burk376:H281DRAFT_01031 Length = 377 Score = 181 bits (458), Expect = 3e-50 Identities = 107/311 (34%), Positives = 166/311 (53%), Gaps = 18/311 (5%) Query: 21 SVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIF--MNMVKPLTLVDGKIFLRVNGEF 78 +V AV+ +SF + E +VGESGCGK+TL ++ ++ + L G+ G Sbjct: 39 TVHAVNEVSFAVHTGETFAIVGESGCGKSTLGRMLLRLIDATQGRVLYQGEDITHWQG-- 96 Query: 79 VELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHGIDEE--ELLDK 136 +L + RD + II Q +L P + + + + HG+ E ++ Sbjct: 97 AKLRRLRRD----------MQIIFQDPFASLNPGMTVGQIIGEPVAFHGLASSGSECRER 146 Query: 137 ARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVL 196 + +VGL P + +RYP E SGG RQR IA A P L++ DEP SALDV Q + Sbjct: 147 VAQLLTKVGLQPAYAQRYPHEFSGGQRQRIGIARALAGEPKLIVGDEPVSALDVSVQAQV 206 Query: 197 LKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQ 256 + +L +K + + ++I + HD+A +R ++DR+ +MY G+IVE A V+ L + PLHPYTQ Sbjct: 207 INLLESLKAE-LGLTLIMVAHDLAVIRHMSDRVAVMYLGEIVELAQVDELFDAPLHPYTQ 265 Query: 257 GLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEP 316 L ++ P ++R + G P+ PP GCRFH RCPHA C ++ P + Sbjct: 266 ALLRAIPASSPH-ERRTKPALQGDLPSPTAPPPGCRFHTRCPHAKPRCVQERPLSETLPG 324 Query: 317 GRRVACWLYME 327 GR+VAC + + Sbjct: 325 GRQVACHFWRD 335 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: 309 Number of extensions: 17 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: 377 Length adjustment: 29 Effective length of query: 301 Effective length of database: 348 Effective search space: 104748 Effective search space used: 104748 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