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 Dsui_2799 Dsui_2799 oligopeptide/dipeptide ABC transporter, ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__PS:Dsui_2799 Length = 670 Score = 306 bits (783), Expect = 1e-87 Identities = 154/318 (48%), Positives = 218/318 (68%), Gaps = 10/318 (3%) Query: 13 LLQTVDLKKYFPQGKRI-------LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILK 65 LL +LK +FP K + +KAVDG+S+E++ G TL LVGESGCGK+T G+ +L+ Sbjct: 351 LLAVGELKVHFPIRKGLFKRTVGHVKAVDGVSLELQRGRTLALVGESGCGKTTAGKAVLR 410 Query: 66 LLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHK 125 LL P G + +G+++ L ++E+KP R++MQ++FQDP SLNP++TVG IIE+ + + Sbjct: 411 LL-PATGSVRLDGRELLGLPERELKPLRRRMQMVFQDPFASLNPRLTVGEIIEEGMTALR 469 Query: 126 IGTKK-ERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 + + ERR + LL+ VG+ E + +PHEFSGGQ+QRI IARALA+ P+ +VCDEP Sbjct: 470 VAASRDERRAALAALLESVGLPAEALGRYPHEFSGGQRQRIAIARALAVQPELLVCDEPT 529 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALDVS+QAQI++LL +Q+++G++YLFI HN AVVE+++H VAVMYLG+IVE G V ++ Sbjct: 530 SALDVSVQAQILNLLRRLQEELGLAYLFITHNFAVVEYLAHDVAVMYLGRIVEQGPVQQV 589 Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFE 304 P HPYTRALL +VP+ GQ++ L GE PSP P+GC F RC + C + Sbjct: 590 LAAPCHPYTRALLSAVPEPRLAGQRE-MVRLPGETPSPARPPQGCHFHPRCAQASERCRQ 648 Query: 305 KEPELTEVEKNHFVSCHL 322 + P + V CHL Sbjct: 649 EYPAPSTQAGGVVVRCHL 666 Score = 222 bits (566), Expect = 2e-62 Identities = 129/321 (40%), Positives = 182/321 (56%), Gaps = 9/321 (2%) Query: 10 MKPLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLL-- 67 M LL +LK F G R+L AVDG+S + GET L+GESGCGKS +L+LL Sbjct: 1 MSDLLSVRNLKAGFLAGGRVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPN 60 Query: 68 --RPDGGKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 R GG+++ EG++I L + M+ R +IFQ+P SLNP +T+GR I + L H Sbjct: 61 AGRIQGGEVWLEGEEILALPEAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLERH 120 Query: 125 KIGTKKERRKRVEELLDMVGIG--REFINSFPHEFSGGQQQRIGIARALALNPKFIVCDE 182 + + R+ LL VGI + +P + SGG +QR IA ALA P+ ++ DE Sbjct: 121 RGMKGEAARREALALLTAVGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPRLLIADE 180 Query: 183 PVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVD 242 P +ALDV+IQAQI+DLL +Q + + L I H+L VV +H+V VMY G+IVE Sbjct: 181 PTTALDVTIQAQILDLLARLQAERAMGMLLITHDLGVVARSAHRVGVMYAGEIVETAPRQ 240 Query: 243 KIFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAIC 302 + F +P HPYT+ L ++P + G + ++ G++P +P GCRF RC C Sbjct: 241 EFFASPRHPYTQKLFAALPDLGQRG--AQLATIPGQVPGLAAMPAGCRFAPRCPVAMDRC 298 Query: 303 FEKEPELTEVEKNHFVSCHLV 323 + P TE+E H V CH V Sbjct: 299 RLESPGWTELEAGHQVRCHWV 319 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: 627 Number of extensions: 24 Number of successful extensions: 9 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: 670 Length adjustment: 33 Effective length of query: 295 Effective length of database: 637 Effective search space: 187915 Effective search space used: 187915 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: 51 (24.3 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