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 5210055 Shew_2502 ABC transporter-related protein (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__PV4:5210055 Length = 261 Score = 108 bits (269), Expect = 2e-28 Identities = 79/264 (29%), Positives = 139/264 (52%), Gaps = 20/264 (7%) Query: 1 MKEILLKAENVR-----AYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVI 55 MK LLK + Y ++ A++ +SFE+ E + +VGE+G GK+TL+ ++ Sbjct: 1 MKSPLLKVNRLSKTFFAGYKGFKRQYNHALEPISFELNRGETLAIVGETGSGKSTLARIL 60 Query: 56 FMNMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRM 115 V DG+I GE +E ++ K + I +I Q +L P + + Sbjct: 61 ----VGAEQRTDGEILFE--GEALESRNL-------KQRCRLIRMIFQDPNTSLNPRLTV 107 Query: 116 EKYVRH-LAESHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATIL 174 + + L + +D++ + +VGL P YP +S GM+QR +A A +L Sbjct: 108 GELLDEPLRFNTDLDKQARFAQVVDTLRKVGLLPEHADFYPHMISEGMKQRVAVARALML 167 Query: 175 NPSLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYA 234 NP ++IADE +ALD+ + +L +L+++ +Q + S IF++H++ +R +D++++++ Sbjct: 168 NPKIIIADEALTALDLSVRSQILNLLLKL-QQEMGLSYIFVSHNMNIIRHFSDKIMVLHQ 226 Query: 235 GKIVEFAPVESLLEKPLHPYTQGL 258 GK+VE A E L P H YTQ L Sbjct: 227 GKMVEKATTEKLFNAPEHEYTQRL 250 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: 204 Number of extensions: 10 Number of successful extensions: 3 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: 261 Length adjustment: 26 Effective length of query: 304 Effective length of database: 235 Effective search space: 71440 Effective search space used: 71440 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: 48 (23.1 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