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 GFF2021 Psest_2064 ABC-type uncharacterized transport system, duplicated ATPase component
Query= TCDB::Q9WXN5 (330 letters) >FitnessBrowser__psRCH2:GFF2021 Length = 553 Score = 134 bits (338), Expect = 4e-36 Identities = 86/265 (32%), Positives = 150/265 (56%), Gaps = 20/265 (7%) Query: 5 LLKAENVRAYYKLEKV-------SVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFM 57 LL+ +++R ++ ++K +KAVDG++F + + + +G+VGESG GK+TL I Sbjct: 279 LLEVDDLRVWFPIKKGLLRRTVDHIKAVDGVNFSLPKGQTLGIVGESGSGKSTLGLAI-- 336 Query: 58 NMVKPLTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEK 117 L L+ + +R G+ L SM++ +V+ +++ ++ Q +L P + + + Sbjct: 337 -----LRLLGSRGEIRFQGQ--HLQSMSQRQVRPL--RRQMQVVFQDPFGSLSPRMSVGQ 387 Query: 118 YVRHLAESHGIDEEELLDKAR-RRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNP 176 V H + + ++A EVGLDP RYP E SGG RQR IA A +L P Sbjct: 388 IVGEGLHIHRMGNAKEQEQAIIEALVEVGLDPETRHRYPHEFSGGQRQRIAIARALVLKP 447 Query: 177 SLLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGK 236 +L++ DEPTSALD Q+ ++++L ++ + + + +FI+HD+A VR ++ +M+++ G+ Sbjct: 448 ALILLDEPTSALDRTVQRQVVELLRSLQAKYNL-TYLFISHDLAVVRALSHQMMVVKQGQ 506 Query: 237 IVEFAPVESLLEKPLHPYTQGLFNS 261 +VE + P HPYTQ L S Sbjct: 507 VVEQGAAADIFAAPQHPYTQQLLES 531 Score = 134 bits (336), Expect = 7e-36 Identities = 94/272 (34%), Positives = 143/272 (52%), Gaps = 29/272 (10%) Query: 23 KAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT-------LVDGKIFLRVN 75 + V+G++F+I + E + +VGESG GK+ ++ I + PL L G+ L+ + Sbjct: 28 RVVEGVTFDIRKGETLALVGESGSGKSVTAHSILRLLPYPLARHPQGQILFHGQDLLKAD 87 Query: 76 GEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAESH-GIDEEELL 134 ++ RK G I ++ Q M +L P + K + + E H G+ + Sbjct: 88 -----------EKAMRKIRGNRIAMVFQEPMTSLNPLHTVGKQINEVLEIHKGLRGKAAT 136 Query: 135 DKARRRFEEVGLDP--LWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEPTSALDVVN 192 + E VG+ I+ YP ELSGG RQR VIA+A P LLIADEPT+ALDV Sbjct: 137 ARTLELLELVGIPEPRKRIRAYPHELSGGQRQRVVIAMALANEPELLIADEPTTALDVTV 196 Query: 193 QKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVEFAPVESLLEKPLH 252 Q +L++L +++ + + +++ I+HD+ VR+IA R+ +M G++VE A E L P H Sbjct: 197 QLKILELLKELQAR-LGMALLLISHDLNLVRRIAHRVCVMQRGRVVEQALCEDLFRAPQH 255 Query: 253 PYTQGLFNSVLTPEPEVKKRGITTIPGAPPNL 284 PYTQ L L EP G + APP L Sbjct: 256 PYTQEL----LAAEP---SGGPVAVEEAPPLL 280 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: 470 Number of extensions: 20 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: 330 Length of database: 553 Length adjustment: 32 Effective length of query: 298 Effective length of database: 521 Effective search space: 155258 Effective search space used: 155258 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: 51 (24.3 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