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 RR42_RS35215 RR42_RS35215 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Cup4G11:RR42_RS35215 Length = 329 Score = 206 bits (523), Expect = 8e-58 Identities = 126/335 (37%), Positives = 186/335 (55%), Gaps = 22/335 (6%) Query: 1 MKEILLKAENVRAYY--------KLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLS 52 M + +L+ EN++ ++ K + SVKAVDG+SF + E +G+VGESGCGK+T Sbjct: 1 MGDEILRVENLKVHFPVTQGVFIKRQVGSVKAVDGVSFTLRRGETLGLVGESGCGKSTTG 60 Query: 53 NVIFMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPT 112 I +K L G+I +F S + + K + + + ++ Q +L P Sbjct: 61 LAI----IKMLAASGGRIAFD-GDDFATFS-----KAQEKNFRRSVQMVYQDPFGSLNPR 110 Query: 113 IRMEKYVRHLAESHGI--DEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAI 170 +++ + E HG+ D E + + VGL P RYP E SGG RQR IA Sbjct: 111 MKVCDIIGEPLEVHGMANDREHYRARIAELLQMVGLLPYMADRYPHEFSGGQRQRIGIAR 170 Query: 171 ATILNPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMI 230 A + PSL++ DEP SALDV Q ++ V M+++R+ + + IFI HD+A VR I+DR+ Sbjct: 171 ALAVEPSLIVCDEPVSALDVSIQAQVVNVFMELQRR-LGLTYIFIAHDLAVVRHISDRIA 229 Query: 231 IMYAGKIVEFAPVESLLEKPLHPYTQGLFNSVLTPEPEVK-KRGITTIPGAPPNLINPPS 289 +MY G+IVE A ++L P HPYT+ L ++V E + KR + G P+ +NPPS Sbjct: 230 VMYLGRIVEIASRDALYANPRHPYTKALLSAVPVASVEAEAKRQRIVLKGEVPSPLNPPS 289 Query: 290 GCRFHPRCPHAMDVCKEKEPPLTEIEPGRRVACWL 324 GCRFHPRC A C+ ++P L E G+ VAC L Sbjct: 290 GCRFHPRCAQATQRCRVEDPVLRERGDGQMVACHL 324 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: 297 Number of extensions: 16 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: 329 Length adjustment: 28 Effective length of query: 302 Effective length of database: 301 Effective search space: 90902 Effective search space used: 90902 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