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_2236 Synpcc7942_2236 ATPase
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__SynE:Synpcc7942_2236 Length = 554 Score = 154 bits (388), Expect = 5e-42 Identities = 86/254 (33%), Positives = 149/254 (58%), Gaps = 7/254 (2%) Query: 9 LTKIFSLGFFSKRR---IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSG 65 L ++ LG + R +AV+N+SF + + LVGESG GK++ A+ ++ L+P + G Sbjct: 300 LLQVEQLGITYRGRSTAFQAVQNLSFTLPAGLTLGLVGESGCGKSSLARCLVGLVPASEG 359 Query: 66 EIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSN 125 +I+ + + + D++ R+ V VFQDP A+ +P + V + + + + + + Sbjct: 360 QIWLDQQPL--DLRSSRDRQRLRQTVQMVFQDPAAALDPRWTVGSAILEPLRIKQPRRDR 417 Query: 126 KKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMI 185 + L+K+ L RV + P D+ +YPH+ SGGQ+QRI IAR I +P L++ DE S + Sbjct: 418 TADQ-RLLKQWLQRVDL-PTDIGDRYPHEFSGGQRQRICIARALIGQPRLLICDESVSAL 475 Query: 186 DASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLE 245 D S + I+ LL++L+ E G + +FI+HDL + Y+SD I VM G++ E +++ Sbjct: 476 DVSVQAQILNLLKQLQAELGLTYLFISHDLAVVRYMSDRILVMNQGQLEEDSPTEQLFQR 535 Query: 246 PTHEYTKLLVGSIP 259 P +YT+ L+ +IP Sbjct: 536 PQSDYTRRLIAAIP 549 Score = 139 bits (349), Expect = 2e-37 Identities = 87/251 (34%), Positives = 145/251 (57%), Gaps = 17/251 (6%) Query: 25 AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPT---SGEIYFEG------KDIW 75 A++ + V+ E V +VGESGSGK+ I LLP T SG+I F +D+ Sbjct: 20 ALQGLDLVVQPGESVGIVGESGSGKSVACLAIPGLLPKTARCSGQIAFRSVAGQSSRDLL 79 Query: 76 KDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEA----LE 131 + +RE ++ +FQ+P +S NP + L +AI ++ P ++ EA + Sbjct: 80 T-LPERELRQLRGDRLGFIFQEPLSSLNPVFSAGFQLLEAIQ--QHLPLSQAEAQQRVIA 136 Query: 132 LIKE-SLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSR 190 L++E L R +L +YPHQ+SGGQ+QR+MIA P L++ADEPT+ +DA+ + Sbjct: 137 LLQEVQLIREPSQAAQILRRYPHQLSGGQRQRLMIAIALAANPDLLLADEPTTALDATVQ 196 Query: 191 GGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEY 250 +++LL L++++ ++IF++HDLG+ V+D + V+ G++VE+G V+ P H Y Sbjct: 197 ASVLQLLRRLQQQRQMAMIFVSHDLGVIAEVADRVVVLYRGQVVEQGRVADVLNSPQHPY 256 Query: 251 TKLLVGSIPKL 261 T+ LV P++ Sbjct: 257 TQGLVACRPQI 267 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: 357 Number of extensions: 15 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: 554 Length adjustment: 30 Effective length of query: 238 Effective length of database: 524 Effective search space: 124712 Effective search space used: 124712 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