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 GFF2391 PS417_12190 microcin ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__WCS417:GFF2391 Length = 531 Score = 241 bits (616), Expect = 2e-68 Identities = 124/255 (48%), Positives = 178/255 (69%), Gaps = 8/255 (3%) Query: 12 PLLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64 PLL+ +LK +FP K L KAVDGI+ + +G+TLG+VGESG GKSTLG IL Sbjct: 274 PLLEVDNLKVWFPIKKGFLRNTVDYVKAVDGINFSLPQGQTLGIVGESGSGKSTLGLAIL 333 Query: 65 KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 +L+ GG I FEG+ + L+ ++++P R++MQ++FQDP GSL+P+M V I+ + L IH Sbjct: 334 RLIASKGG-IRFEGQQLDTLSQQQVRPLRREMQVVFQDPFGSLSPRMCVSEIVGEGLRIH 392 Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 K+GT E+ + L VG+ E + +PHEFSGGQ+QRI IARAL L P+ I+ DEP Sbjct: 393 KMGTPAEQEAAIIAALKEVGLDPESRHRYPHEFSGGQRQRIAIARALVLKPRLILLDEPT 452 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALD ++Q Q+++LL +Q K ++YLFI+H+LAVV+ +SH++ V+ G++VE GD +I Sbjct: 453 SALDRTVQRQVVELLRSLQTKYNLTYLFISHDLAVVKALSHQLMVVKHGQVVEQGDAAEI 512 Query: 245 FLNPIHPYTRALLKS 259 F P H YTR LL++ Sbjct: 513 FAAPQHGYTRQLLEA 527 Score = 194 bits (493), Expect = 4e-54 Identities = 107/257 (41%), Positives = 163/257 (63%), Gaps = 8/257 (3%) Query: 13 LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL----- 67 L++ DL F G + V+ +S +IK GET+ LVGESG GKS +IL+LL Sbjct: 6 LIEIRDLSVEFVTGDHHHRVVNNVSFDIKRGETIALVGESGSGKSVTAHSILRLLPYPLA 65 Query: 68 RPDGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 R G I + G+D+ L +K ++ R ++ +IFQ+P+ SLNP ++ + I + L +HK Sbjct: 66 RHPSGTINYAGQDLLTLKEKTIRHIRGNRIAMIFQEPMTSLNPLHSIEKQINEVLGLHKG 125 Query: 127 GTKKERRKRVEELLDMVGIGREF--INSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 K +R ELLD+VGI + + PHE SGGQ+QR+ IA ALA P+ ++ DEP Sbjct: 126 LQGKVATQRTLELLDLVGIPEPHKRLKALPHELSGGQRQRVMIAMALANEPELLIADEPT 185 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 +ALDV++Q +I++LL+E+Q ++G++ L I+H+L +V I+H+V VM G IVE D + + Sbjct: 186 TALDVTVQLKILELLKELQARLGMALLLISHDLNLVRRIAHRVCVMQKGCIVEQADCETL 245 Query: 245 FLNPIHPYTRALLKSVP 261 F +P HPYT+ LL + P Sbjct: 246 FQSPQHPYTQELLAAEP 262 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: 492 Number of extensions: 26 Number of successful extensions: 7 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: 531 Length adjustment: 31 Effective length of query: 297 Effective length of database: 500 Effective search space: 148500 Effective search space used: 148500 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