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 Synpcc7942_1305 Synpcc7942_1305 ATPase
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__SynE:Synpcc7942_1305 Length = 536 Score = 168 bits (426), Expect = 2e-46 Identities = 90/242 (37%), Positives = 152/242 (62%), Gaps = 9/242 (3%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRE 82 + AV +S EV E + L+GESG GK+T + IL+LL P+ G++ F+G+D+ + + DR Sbjct: 297 VRAVDGLSLEVWPGETLGLIGESGCGKSTLLRTILQLLRPSQGKVLFQGQDLTQ-LPDRR 355 Query: 83 SLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISL--LENKPSNKKEALELIKESLFRV 140 L RR++ +FQDP A NP + + + + L + K++ L ++++ V Sbjct: 356 -LRSLRRELQLIFQDPAACLNPRLTIGDAIADPLKIQGLARGAAAKQQVLAILEQ----V 410 Query: 141 GIDPKDV-LGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199 G+ P + +YPHQ+SGGQ+QR+ IAR I RP L++ DEP SM+DA+ + ++ L++E Sbjct: 411 GLTPAPTWIDRYPHQLSGGQQQRVAIARALITRPKLVLCDEPVSMLDATVQAQVLALMQE 470 Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIP 259 L+++ + +F+THDL +A D + V++ G+IVE G +V+ +P H YT+ L+ S+P Sbjct: 471 LKQQLNLTYLFVTHDLRVAREFCDRVAVLQRGKIVEIGPAAQVLTQPEHPYTRSLLASLP 530 Query: 260 KL 261 +L Sbjct: 531 EL 532 Score = 135 bits (340), Expect = 2e-36 Identities = 88/238 (36%), Positives = 135/238 (56%), Gaps = 10/238 (4%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTS---GEIYFEGKDIWKDIKDR 81 A++ +S E+ E + LVGESG GK+T + ILRLLPP S G+I G+ + + Sbjct: 20 ALQQLSLELAAGERLGLVGESGCGKSTLGRAILRLLPPGSHQQGDIRLAGQALGQ--LQG 77 Query: 82 ESLVEFRR-KVHAVFQDPFASYNPFYPVERTLWQAISLLENKPS-NKKEALELIKESLFR 139 SL FR +V VFQDP +P + L + + + ++P ++++A + L R Sbjct: 78 RSLQRFRGGQVGLVFQDPMTRLDPLQTIGDHLLETLQV--HRPHLSRRQAKQQALSWLER 135 Query: 140 VGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199 V I P + +YPHQ SGG +QR+ IA +L+P L+VADEPT+ +D + I++ L Sbjct: 136 VRI-PANRWSQYPHQFSGGMRQRVAIALALLLQPRLVVADEPTTSLDVTVAAEILQELTR 194 Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGS 257 L E+ TS++ I+HDL + D I V+ G++VE G V+ P H YT+ L+ S Sbjct: 195 LCSEENTSLLLISHDLPMVAAYCDRIAVLYQGQLVETGPTTAVLTRPQHPYTQTLLQS 252 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: 338 Number of extensions: 13 Number of successful extensions: 5 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: 536 Length adjustment: 30 Effective length of query: 238 Effective length of database: 506 Effective search space: 120428 Effective search space used: 120428 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