Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_011386731.1 AMB_RS22185 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >NCBI__GCF_000009985.1:WP_011386731.1 Length = 533 Score = 224 bits (570), Expect = 5e-63 Identities = 120/248 (48%), Positives = 171/248 (68%), Gaps = 9/248 (3%) Query: 18 DLKKYFPQGKRI-------LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPD 70 DLK +FP + +KAVDGIS+++K G T+G+VGESG GK+TLG +L+LL D Sbjct: 278 DLKVWFPLKAGLWRKTVGHVKAVDGISLDLKRGHTIGVVGESGSGKTTLGLALLRLLDSD 337 Query: 71 GGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKK 130 G +I F G I +++ ++P R++MQ++FQDP GSL+P+M+VG+I+ + L +H+ Sbjct: 338 G-EISFGGTRIESMSAGTLRPLRRQMQMVFQDPYGSLSPRMSVGQIVGEGLEVHEPAMHA 396 Query: 131 ERRKR-VEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDV 189 R R + L+ VG+ + +PHEFSGGQ+QRI IARAL L PKFIV DEP SALDV Sbjct: 397 AERDRLIAAALEEVGLDPATRDRYPHEFSGGQRQRIAIARALVLKPKFIVLDEPTSALDV 456 Query: 190 SIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPI 249 S+QAQI+DLL ++Q + ++YLFI+H+L VV ++ + VM GK+VE G D++F P Sbjct: 457 SVQAQIVDLLRDLQARHALAYLFISHDLRVVRALADDLLVMKDGKVVEAGRADELFKAPR 516 Query: 250 HPYTRALL 257 YTRAL+ Sbjct: 517 TAYTRALM 524 Score = 173 bits (439), Expect = 8e-48 Identities = 104/259 (40%), Positives = 156/259 (60%), Gaps = 12/259 (4%) Query: 12 PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL---- 67 PLL DL F ++AV G+S + +GETL LVGESG GKS +IL+LL Sbjct: 6 PLLVVDDLAVSFGP----VQAVKGVSFTLAKGETLALVGESGSGKSVTALSILQLLPYPR 61 Query: 68 -RPDGGKIFFEGKDITNLNDKEMKPYRK-KMQIIFQDPLGSLNPQMTVGRIIEDPLIIHK 125 G I +G ++ + ++ R ++ ++FQ+P+ SLNP ++ + + L +H Sbjct: 62 ATHPRGSIRLDGAELVGAPEPALRKVRGGRIAMVFQEPMTSLNPLHSIEAQVGEVLELHL 121 Query: 126 IGTKKERRKRVEELLDMVGIGR--EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEP 183 R RV ELL +VGI + + + PHE SGGQ+QR+ IA ALA P ++ DEP Sbjct: 122 GLRGSTLRDRVVELLSLVGIPEPEKRLGALPHELSGGQRQRVMIAMALAGEPDILIADEP 181 Query: 184 VSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDK 243 +ALDV+IQAQI+ LL+ +Q ++G++ LFI H+L +V ++ +V VM G+IVE G + + Sbjct: 182 TTALDVTIQAQILALLKGLQARLGMALLFITHDLGIVRKMADRVCVMNAGEIVESGPLPQ 241 Query: 244 IFLNPIHPYTRALLKSVPK 262 +F P HPYT+ LL + PK Sbjct: 242 VFDAPAHPYTQRLLAAEPK 260 Lambda K H 0.321 0.142 0.417 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: 508 Number of extensions: 29 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: 328 Length of database: 533 Length adjustment: 32 Effective length of query: 296 Effective length of database: 501 Effective search space: 148296 Effective search space used: 148296 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: 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