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 GFF2860 HP15_2804 oligopeptide/dipeptide ABC transporter, ATP-binding protein-like protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Marino:GFF2860 Length = 672 Score = 167 bits (424), Expect = 4e-46 Identities = 97/243 (39%), Positives = 148/243 (60%), Gaps = 9/243 (3%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGE----IYFEGKDIWKDI 78 + AV+ +S E+ E + +VGESGSGK+ TA ++ LLPP + I F+G D+ Sbjct: 23 LHAVRGISLELNRGETLGIVGESGSGKSMTALALMNLLPPAAKRQASCIDFDGSDL-THA 81 Query: 79 KDRESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESL 137 +RE + R +++ +FQ+P S NP Y + R L + ++L ++ + EA L Sbjct: 82 TERELASKIRGQRIGMIFQEPMTSLNPVYSIGRQLKETMTL--HRKVSDTEAENRAVYLL 139 Query: 138 FRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKL 196 +VG+ DP L +YPH++SGGQ+QR+MIA + P L++ADEPT+ +D + + I+ L Sbjct: 140 EKVGLPDPASRLKQYPHELSGGQRQRVMIAMALMNEPELLIADEPTTALDVTIQAQILHL 199 Query: 197 LEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVG 256 L EL++E G S+I ITHDLG+ +DNI VM G+IVE G +V+ P H YTK L+ Sbjct: 200 LRELQQEFGMSMILITHDLGVVSRAADNIAVMYAGDIVETGKTGEVLENPRHPYTKGLLE 259 Query: 257 SIP 259 +P Sbjct: 260 CVP 262 Score = 160 bits (404), Expect = 9e-44 Identities = 95/261 (36%), Positives = 158/261 (60%), Gaps = 19/261 (7%) Query: 4 LVVKNLTKIFSL--GFFSKRR-IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 L V +++ FS+ G F KR+ ++A+ +VS +K+ E+++LVGESG GKTT + I+ L Sbjct: 353 LTVDHVSCTFSVRRGMFGKRKPLQALDDVSLTLKKGEVLALVGESGCGKTTLTRTIMGLQ 412 Query: 61 PPTSGEIYFEGKDIWKDIKDRESL--VEFRRKVHAVFQDPFASYNPFYPVERTLWQAIS- 117 P++G + G+ I E+L ++ R + +FQDP++S NP +T+ + I+ Sbjct: 413 APSTGSVTLNGQRI-------ENLPPMDRARMIQPIFQDPYSSLNP----RKTIGEIIAK 461 Query: 118 -LLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLI 176 L + + +E + +++ + VG+ P V YP Q+SGGQ+QR I R IL P ++ Sbjct: 462 PLFVHGIGSNQEQHQQVRKMMELVGL-PSRVFNSYPDQLSGGQRQRAAIGRALILNPEVV 520 Query: 177 VADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVER 236 + DEPTS +D S + I+ LL +LR+E + +F+TH+L + +++D + VM GEIVE Sbjct: 521 ICDEPTSALDVSVQAQILNLLLDLRDELDLTYLFVTHNLSVVQHMADRVAVMYLGEIVEC 580 Query: 237 GHPDKVVLEPTHEYTKLLVGS 257 G D+V+ +P H YT L+ S Sbjct: 581 GERDQVMSDPKHPYTHALMNS 601 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: 444 Number of extensions: 18 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 268 Length of database: 672 Length adjustment: 32 Effective length of query: 236 Effective length of database: 640 Effective search space: 151040 Effective search space used: 151040 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: 50 (23.9 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