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 3607243 Dshi_0658 ABC transporter related (RefSeq)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Dino:3607243 Length = 533 Score = 220 bits (561), Expect = 5e-62 Identities = 113/250 (45%), Positives = 170/250 (68%), Gaps = 8/250 (3%) Query: 15 QTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL 67 +T LK +FP + IL KAV+ ++ ++ GETLG+VGESG GK+TL IL+L+ Sbjct: 275 ETDSLKVWFPIQRGILRRTVGHVKAVNNATLNVRAGETLGVVGESGSGKTTLALAILRLI 334 Query: 68 RPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127 +G +I + G++I ++++ RK MQ++FQDP GSL+P+MT+ +II + L +H + Sbjct: 335 SSEG-RIVYAGENIQGWKSRDLRRLRKDMQVVFQDPYGSLSPRMTIAQIIAEGLGVHGLE 393 Query: 128 TKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSAL 187 + R+ V E+L VG+ ++ +PHEFSGGQ+QRI IARA+ L PK +V DEP SAL Sbjct: 394 PGADPRRMVAEILVEVGLDPAMMDRYPHEFSGGQRQRIAIARAMILRPKLVVLDEPTSAL 453 Query: 188 DVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLN 247 D+++Q QI++LL +Q+K G++Y+FI+H+L VV +SHKV VM G +VE G+ +IF Sbjct: 454 DMTVQVQIVELLRALQRKYGLAYIFISHDLKVVRALSHKVIVMRQGDVVEMGEGRQIFER 513 Query: 248 PIHPYTRALL 257 P YT+ LL Sbjct: 514 PRSDYTKQLL 523 Score = 191 bits (486), Expect = 3e-53 Identities = 108/256 (42%), Positives = 161/256 (62%), Gaps = 8/256 (3%) Query: 13 LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG- 71 +LQ +L+ F Q ++ +AV G+S ++ +GET+ LVGESG GKS + + LL PD Sbjct: 5 VLQVRNLRVGFRQDGQVTEAVKGVSFDVAQGETVALVGESGSGKSVTALSTVSLL-PDSA 63 Query: 72 ---GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127 G I + G ++ +++++ R + IFQ+P+ SLNP + + I + L +H+ Sbjct: 64 EVSGSITYAGTEMVGAPERDLRRVRGNDVSFIFQEPMTSLNPLHPLEKQITESLTLHQGL 123 Query: 128 TKKERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVS 185 T R RV ELL+ VGI + ++PH+ SGGQ+QR+ IA ALA P ++ DEP + Sbjct: 124 TGDAARARVIELLEKVGIRDAESRLGAYPHQLSGGQRQRVMIAMALANGPDLLIADEPTT 183 Query: 186 ALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245 ALDV+IQAQI+DLL ++++ G+S LFI H+L +V I+ +V VM G+IVE G +IF Sbjct: 184 ALDVTIQAQILDLLADLKEAEGMSLLFITHDLTIVRRIADRVCVMQGGEIVETGPTAEIF 243 Query: 246 LNPIHPYTRALLKSVP 261 NP HPYTR LL + P Sbjct: 244 ANPQHPYTRKLLAAEP 259 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: 471 Number of extensions: 24 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: 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