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 Pf1N1B4_5629 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5629 Length = 524 Score = 235 bits (600), Expect = 2e-66 Identities = 116/233 (49%), Positives = 169/233 (72%), Gaps = 1/233 (0%) Query: 25 QGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNL 84 Q K L+AVDGIS+ ++ G+TLG+VGESG GKSTLG+ IL+LL +G I F+G+ + L Sbjct: 287 QRKTYLRAVDGISLNVQRGKTLGIVGESGSGKSTLGQAILRLLDSEGS-IRFQGEALDGL 345 Query: 85 NDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVG 144 K+++P+RKKMQ++FQDP GSL+P+M+V +II + L +H T E +V +L+ VG Sbjct: 346 TQKQLRPWRKKMQVVFQDPFGSLSPRMSVAQIISEGLEVHSQSTPDECEAQVIRVLEEVG 405 Query: 145 IGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQ 204 + + + +PHEFSGGQ+QRI IARAL L P I+ DEP SALD ++Q Q++ LL ++Q+ Sbjct: 406 LDPQSRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSALDRTVQKQVVALLRQLQE 465 Query: 205 KMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALL 257 K G++YLFI+H+LAV+ ++H + V+ GK+VE G +F +P HPYT+ LL Sbjct: 466 KYGLTYLFISHDLAVIRALAHDMIVIKDGKVVESGASHDVFDSPQHPYTKELL 518 Score = 179 bits (453), Expect = 2e-49 Identities = 96/237 (40%), Positives = 154/237 (64%), Gaps = 7/237 (2%) Query: 33 VDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG----GKIFFEGKDITNLNDKE 88 V + ++I+ GE L LVGESGCGKS +IL+LL G G I + G+++ + K Sbjct: 21 VRNLCLDIRPGECLALVGESGCGKSVTAHSILQLLPETGTETTGSIRYRGQELIGTDIKT 80 Query: 89 MKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGR 147 ++ R ++ +IFQ+P+ SLNP +V + I + L++H+ K + R+ ELL +VGI + Sbjct: 81 LRELRGNRIAMIFQEPMTSLNPLHSVEKQIGETLLLHRGLGGKAAQARILELLQLVGIQK 140 Query: 148 --EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQK 205 E + ++PH+ SGGQ+QR+ IA ALA P+ ++ DEP +ALDV++Q +I+ LL+ +QQ+ Sbjct: 141 PEERLKAYPHQLSGGQRQRVMIAMALACEPELLIADEPTTALDVTVQRKILLLLKSLQQR 200 Query: 206 MGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPK 262 +G+S L I+H+L +V I+ +V VM G+IVE + +F P HPY+ LL + P+ Sbjct: 201 LGMSLLLISHDLNLVRSIAQRVCVMKAGEIVEQAPCETLFTEPKHPYSCVLLHAEPE 257 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: 515 Number of extensions: 16 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: 328 Length of database: 524 Length adjustment: 31 Effective length of query: 297 Effective length of database: 493 Effective search space: 146421 Effective search space used: 146421 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