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 RR42_RS21365 RR42_RS21365 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Cup4G11:RR42_RS21365 Length = 545 Score = 171 bits (434), Expect = 2e-47 Identities = 103/263 (39%), Positives = 153/263 (58%), Gaps = 17/263 (6%) Query: 4 LVVKNLTKIFSLG---FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 L V++L K +S G F KR + AV VSF V+ + + +VGESGSGK+T K +L+L Sbjct: 280 LEVRDLRKTYSSGGGLFSKKRVVNAVDGVSFSVRRGQTLGIVGESGSGKSTIGKCLLKLT 339 Query: 61 PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAI---- 116 GE+ F+G+DI + + +R+ R V +FQDPFAS NP + V R + Sbjct: 340 DIDGGELLFDGQDIAR-LTERQ-FRPLRSDVQMIFQDPFASLNPRHTVGRIITDGPIANG 397 Query: 117 SLLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLI 176 + L + +E L+L VG++P +YP+Q SGGQ+QRI IAR L P L+ Sbjct: 398 AALAQAQARGRELLQL-------VGLEPS-AFDRYPNQFSGGQRQRIGIARALALDPKLL 449 Query: 177 VADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVER 236 VADE S +D S + +++LL +L++ +IFITHDL +A + ++ VM G +VE Sbjct: 450 VADESVSALDVSVQAQVLQLLADLQKRLNIGLIFITHDLRVAAQICHHVIVMHKGRVVES 509 Query: 237 GHPDKVVLEPTHEYTKLLVGSIP 259 G PD++ P H YT+ L+ +IP Sbjct: 510 GPPDQIFDAPQHAYTQRLIAAIP 532 Score = 167 bits (424), Expect = 3e-46 Identities = 93/254 (36%), Positives = 155/254 (61%), Gaps = 14/254 (5%) Query: 22 RIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPP----TSGEIYFEGKDIWKD 77 R AVK VS+++ EI+ +VGESGSGK+ +A I+ LLPP G+I F+GKD+ Sbjct: 25 RAHAVKEVSYDLHAGEILCIVGESGSGKSMSANAIMGLLPPYLKPQGGQILFQGKDLLT- 83 Query: 78 IKDRESLVEFRRKVHA-VFQDPFASYNPFYPVERTLWQAISLLENKP--SNKKEALELIK 134 +D ++L+ R K A VFQ+P ++ NP V + + + + + P + K LEL++ Sbjct: 84 -QDEQTLLSMRGKAMAMVFQEPLSALNPVMTVGDQIAEVMRVHDAYPGEARTKRVLELLE 142 Query: 135 ESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGI 193 VG+ DP ++ YP ++SGGQ+QR++IA L P L++ADEPT+ +D +++ I Sbjct: 143 F----VGLPDPATLIHSYPFRLSGGQRQRVVIAMALALEPALLIADEPTTALDVTTQAQI 198 Query: 194 IKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKL 253 + L+ ++ ++G ++F+THD G+ ++D + VM+ G +VE G +V+ P H YT+ Sbjct: 199 LALIRRIQADKGMGVMFVTHDFGVVAEIADRVAVMERGVLVEVGPVQQVLNHPQHPYTRR 258 Query: 254 LVGSIPKLYRKLED 267 L+G++P K D Sbjct: 259 LIGAVPHGRAKARD 272 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: 359 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: 545 Length adjustment: 30 Effective length of query: 238 Effective length of database: 515 Effective search space: 122570 Effective search space used: 122570 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