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 PfGW456L13_2876 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2876 Length = 525 Score = 236 bits (601), Expect = 1e-66 Identities = 122/251 (48%), Positives = 178/251 (70%), Gaps = 7/251 (2%) Query: 13 LLQTVDLKKYFPQG------KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKL 66 +L+ +L+ FP G K L+AVDGIS+ I+ G+TLG+VGESG GKSTLG+ IL+L Sbjct: 268 VLEVDNLQVRFPVGGGLFQRKTWLRAVDGISLNIQRGKTLGIVGESGSGKSTLGQAILRL 327 Query: 67 LRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 L +GG I F+G+ + L K+++P+RKKMQ++FQDP GSL+P+M+V +II + L +H Sbjct: 328 LDSEGG-IRFQGQALDGLTQKQLRPWRKKMQVVFQDPFGSLSPRMSVAQIISEGLEVHSQ 386 Query: 127 GTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSA 186 + +E V L+ VG+ + + +PHEFSGGQ+QRI IARAL L P I+ DEP SA Sbjct: 387 LSTEECNAEVIRALNEVGLDPQSRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPTSA 446 Query: 187 LDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFL 246 LD ++Q Q++ LL ++Q+K G++YLFI+H+LAVV ++H + V+ GK+VE G ++F Sbjct: 447 LDRTVQKQVVALLRQLQEKYGLTYLFISHDLAVVRALAHDMIVIKDGKVVERGASHEVFD 506 Query: 247 NPIHPYTRALL 257 +P HPYT+ LL Sbjct: 507 SPQHPYTKELL 517 Score = 173 bits (438), Expect = 1e-47 Identities = 98/260 (37%), Positives = 163/260 (62%), Gaps = 11/260 (4%) Query: 10 MKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP 69 M L++ DL F G+ +++ + ++I+ GE L LVGESG GKS +IL+LL Sbjct: 1 MTNLIEIRDLSVAF-SGQTVVR---NLCLDIRPGECLALVGESGSGKSVTAHSILQLLPQ 56 Query: 70 DG----GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 G I + G+++ + +++ R ++ +IFQ+P+ SLNP ++ + I + L++H Sbjct: 57 TDTETTGSIRYRGQELVGADAGKLRKLRGNRIAMIFQEPMTSLNPLHSIEKQIGETLLVH 116 Query: 125 KIGTKKERRKRVEELLDMVGIGR--EFINSFPHEFSGGQQQRIGIARALALNPKFIVCDE 182 K K + R+ ELL +VGI + E + ++PH+ SGGQ+QR+ IA ALA P+ ++ DE Sbjct: 117 KGLAGKAAQARILELLHLVGIQKPEERLKAYPHQLSGGQRQRVMIAMALACEPELLIADE 176 Query: 183 PVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVD 242 P +ALDV++Q +I+ LL+ +QQ++G+S L I+H+L +V I+ +V VM G+IVE + Sbjct: 177 PTTALDVTVQRKILLLLKSLQQRLGMSLLLISHDLNLVRSIAQRVCVMKAGEIVEQAPCE 236 Query: 243 KIFLNPIHPYTRALLKSVPK 262 +F P HPY+ LL + P+ Sbjct: 237 TLFTEPRHPYSCILLHAEPE 256 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: 513 Number of extensions: 13 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: 525 Length adjustment: 31 Effective length of query: 297 Effective length of database: 494 Effective search space: 146718 Effective search space used: 146718 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