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 5210054 Shew_2501 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__PV4:5210054 Length = 337 Score = 119 bits (299), Expect = 7e-32 Identities = 75/245 (30%), Positives = 137/245 (55%), Gaps = 8/245 (3%) Query: 22 RIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPT----SGEIYFEGKDIWKD 77 R++A++ VS + E+ LVGESGSG+T AK IL + + + ++G+++ D Sbjct: 19 RVKALERVSLTLNPGEVHGLVGESGSGRTLLAKAILGIPGHNWTIQADRMMWDGQNLM-D 77 Query: 78 IKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKK--EALELIKE 135 + E V ++ +FQDP +S +P V + +A+ + P K+ + + ++ Sbjct: 78 MSPSERRVLMGSEMAMIFQDPISSLDPAIAVGTQIIEAMPENKELPWWKRGSDKRKKAQQ 137 Query: 136 SLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGII 194 L +VGI + + ++ Y ++S G+ Q++MIA +P L++ADEPT+ ++ ++ I Sbjct: 138 WLHKVGIKETQKIMSSYAWELSDGECQKVMIAIAVANQPRLLIADEPTNSMEVRTQAQIF 197 Query: 195 KLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLL 254 +LL +L + Q SI+ I+H+L D + VM +G+++E G V+ P H YTK L Sbjct: 198 RLLSKLNQLQNVSILLISHELETLSQWCDRLTVMYSGQVMESGVTSDVIANPYHPYTKAL 257 Query: 255 VGSIP 259 + +IP Sbjct: 258 LDNIP 262 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: 196 Number of extensions: 14 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: 337 Length adjustment: 27 Effective length of query: 241 Effective length of database: 310 Effective search space: 74710 Effective search space used: 74710 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