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 8501089 DvMF_1825 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__Miya:8501089 Length = 339 Score = 177 bits (450), Expect = 3e-49 Identities = 108/307 (35%), Positives = 168/307 (54%), Gaps = 15/307 (4%) Query: 18 EKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLTLVDGKIFLRVNGE 77 ++ V AV+ +SF+IL E + VVGESGCGK+TL+ + + G+I R GE Sbjct: 38 KRTVVHAVNDVSFDILPGETLSVVGESGCGKSTLARTV----IGLYRATGGEILYR--GE 91 Query: 78 FVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESH--GIDEEELLD 135 ++ S R + ++ Q +L P +++ + + H GI + ++ Sbjct: 92 RIDNLSDNGMLPYRT----RMQMVFQDPYASLNPRMKVREILEEPVRFHNPGISDADVRA 147 Query: 136 KARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVNQKV 195 + E+VG++PLW RYP E SGG RQR IA A +++P ++ADEP SALDV Q Sbjct: 148 RVADVMEQVGVNPLWGVRYPHEFSGGQRQRISIARALVVDPEFIVADEPISALDVSIQAQ 207 Query: 196 LLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLHPYT 255 +L ++M M+ + + + +FI+HD++ V I+ R+ +MY G + E A E L P HPYT Sbjct: 208 VLNLMMDMQEKRNL-TYLFISHDLSVVEHISTRVAVMYLGSLCELASAEDLFGNPRHPYT 266 Query: 256 QGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPHAMDVCKEKEPPLTEIE 315 + L +++ P K G + G P IN P+GC FH RC HA C ++ P ++E Sbjct: 267 RALLSAI--PRIGGKAAGHIKLSGDVPTPINLPTGCVFHGRCQHANARCMQEVPKARQLE 324 Query: 316 PGRRVAC 322 G +VAC Sbjct: 325 GGAQVAC 331 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: 282 Number of extensions: 8 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: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 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