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 WP_069333144.1 C8J29_RS18800 ATP-binding cassette domain-containing protein
Query= TCDB::Q9WXN5 (330 letters) >NCBI__GCF_003046325.1:WP_069333144.1 Length = 331 Score = 191 bits (486), Expect = 2e-53 Identities = 113/307 (36%), Positives = 170/307 (55%), Gaps = 16/307 (5%) Query: 22 VKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGEFVEL 81 V+AVD +SFE+ E +G+VGESGCGK+TL+ M+ L+ +G L E+ Sbjct: 38 VQAVDRVSFEVAPGETVGIVGESGCGKSTLAK-----MLAGLSGTNGGELLLRGRPLAEV 92 Query: 82 SSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESHG-IDEEELLDKARRR 140 S R +K + ++ PQ+++NA M + + V HG I E + R Sbjct: 93 MSDPRQALKVQMIFQD----PQSSLNARMKVVDI---VGEAPVVHGLIPRAEKEARVRAM 145 Query: 141 FEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKVLLKVL 200 E VGL P + RYP + SGG RQR IA A + P LLI DE +ALDV Q ++ +L Sbjct: 146 LERVGLGPEALHRYPHQFSGGQRQRIGIARALAVEPELLICDESVAALDVSVQAQIINLL 205 Query: 201 MQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYTQGLFN 260 M+++R + +++FI+HD++ +R I DR+I+MY G+ VE AP ++L P HPYT+ L Sbjct: 206 MELRRD-LGLTMLFISHDLSVIRHICDRVIVMYLGRAVEIAPTDALFADPRHPYTRMLLA 264 Query: 261 SVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIEPGRRV 320 + P ++R + G P+ + PP+GC FHPRC + C + PPL ++ R Sbjct: 265 GM--PRISTERRAFLEVAGEIPSPLAPPAGCHFHPRCQFRTEECLAQRPPLDPVDARRSA 322 Query: 321 ACWLYME 327 AC + E Sbjct: 323 ACLRWRE 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: 285 Number of extensions: 13 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: 331 Length adjustment: 28 Effective length of query: 302 Effective length of database: 303 Effective search space: 91506 Effective search space used: 91506 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 24 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