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 PP_4150 PP_4150 microcin C transporter - ATP binding subunit
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Putida:PP_4150 Length = 534 Score = 246 bits (629), Expect = 7e-70 Identities = 126/255 (49%), Positives = 177/255 (69%), Gaps = 8/255 (3%) Query: 12 PLLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64 PLL+ DLK +FP K L KAVDG++ + +G+TLG+VGESG GKSTLG IL Sbjct: 274 PLLEVDDLKVWFPIKKGFLQRTVDHVKAVDGVNFSLPQGQTLGIVGESGSGKSTLGLAIL 333 Query: 65 KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 +L+ GG I F G+++ LN K ++P R++MQ++FQDP GSL+P+M V I+ + L IH Sbjct: 334 RLISSQGG-IRFHGQNLEGLNQKAVRPLRREMQVVFQDPFGSLSPRMCVADIVGEGLRIH 392 Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 +IGT +E+ + L+ VG+ + +PHEFSGGQ+QRI IARAL L P I+ DEP Sbjct: 393 RIGTAQEQEAAIIAALEEVGLDPRTRHRYPHEFSGGQRQRIAIARALVLKPALILLDEPT 452 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALD ++Q Q+++LL +QQK ++YLFI+H+LAVV+ +SH++ V+ G +VE GD I Sbjct: 453 SALDRTVQRQVVELLRNLQQKYNLTYLFISHDLAVVKALSHQLMVIKHGHVVEQGDAQAI 512 Query: 245 FLNPIHPYTRALLKS 259 F P HPYTR LL++ Sbjct: 513 FHAPQHPYTRQLLEA 527 Score = 207 bits (528), Expect = 4e-58 Identities = 112/257 (43%), Positives = 170/257 (66%), Gaps = 8/257 (3%) Query: 13 LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL----- 67 L++ DL F G ++ + VDG+S +I++GETL LVGESG GKS +IL+LL Sbjct: 6 LIEVRDLAVEFVTGDQVNRVVDGVSFDIRKGETLALVGESGSGKSVTAHSILRLLPYPLA 65 Query: 68 RPDGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKI 126 R G I +EGKD+ ++K ++ R ++ +IFQ+P+ SLNP + + I + L++HK Sbjct: 66 RHPSGSIRYEGKDLLQQSEKTLQRIRGNRIAMIFQEPMTSLNPLHCIEKQINEILLLHKG 125 Query: 127 GTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 T KE R ELLDMVGI R+ + + PHE SGGQ+QR+ IA ALA P+ ++ DEP Sbjct: 126 LTGKEATARTLELLDMVGIPEPRKRLKALPHELSGGQRQRVMIAMALANEPELLIADEPT 185 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 +ALDV++Q +I++LL+E+Q +MG++ L I+H+L +V I+H+V VM G+IVE + + Sbjct: 186 TALDVTVQLKILELLKELQARMGMALLLISHDLNLVRRIAHRVCVMQRGQIVEQAECATL 245 Query: 245 FLNPIHPYTRALLKSVP 261 F +P H YT+ L+ + P Sbjct: 246 FSSPQHHYTQMLINAEP 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: 498 Number of extensions: 22 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: 534 Length adjustment: 32 Effective length of query: 296 Effective length of database: 502 Effective search space: 148592 Effective search space used: 148592 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