Align TM0027, 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 AO356_29390 AO356_29390 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29390 Length = 329 Score = 159 bits (403), Expect = 6e-44 Identities = 96/246 (39%), Positives = 146/246 (59%), Gaps = 13/246 (5%) Query: 16 GFFSKRRI-EAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDI 74 GFF I +AV VS + E + LVGESG GK+T AK++L LL PTSG++ GK + Sbjct: 21 GFFKPAAILKAVDGVSLRLMRGETLGLVGESGCGKSTLAKLLLGLLAPTSGDVLVNGKHL 80 Query: 75 WKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISL--LENKPSNKKEALEL 132 DR+ E R + +FQDP++S NP +TL I+L + + + E + Sbjct: 81 --AATDRK---EMARHIQPIFQDPYSSLNP----RKTLRDIITLPLIVHDIGSPAERRKK 131 Query: 133 IKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGG 192 + L VG+ PK V+ YP Q+SGGQ+QR+ IAR I+RP +++ DEPTS +D S + Sbjct: 132 TEAMLDVVGL-PKRVIDSYPSQLSGGQRQRVAIARALIMRPDVLICDEPTSALDVSVQAQ 190 Query: 193 IIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTK 252 I+ LL++L+ E G + + I+H+L + +++D + VM G IVE + + EP H YT+ Sbjct: 191 ILNLLQDLKREFGLTYLLISHNLAVIEHLADRVAVMYLGRIVEERTRESLFAEPGHPYTR 250 Query: 253 LLVGSI 258 L+ S+ Sbjct: 251 ALLDSV 256 Lambda K H 0.319 0.139 0.397 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: 222 Number of extensions: 7 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: 268 Length of database: 329 Length adjustment: 26 Effective length of query: 242 Effective length of database: 303 Effective search space: 73326 Effective search space used: 73326 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 (21.7 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