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 SMa1646 SMa1646 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Smeli:SMa1646 Length = 340 Score = 270 bits (690), Expect = 4e-77 Identities = 140/314 (44%), Positives = 209/314 (66%), Gaps = 7/314 (2%) Query: 12 PLLQTVDLKKYFPQGKR--ILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRP 69 P+L+ +L+ F +R + AVD +SIE+ GE +GLVGESGCGKSTLGRTI+ L + Sbjct: 5 PVLKVENLQTRFKSVQRGKYVHAVDDVSIELYPGEIVGLVGESGCGKSTLGRTIVGLEKA 64 Query: 70 DGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTK 129 G++ +G D+++L+ ++ R+ +Q +FQDP SLN + TVG I++ L+I + Sbjct: 65 TSGRVLLDGVDLSSLSGAALRRSRRALQYVFQDPYSSLNDRQTVGETIDEALLIDGTYSL 124 Query: 130 KERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDV 189 ER +R +ELLD VG+ + E SGGQ+QR+ IAR+LA+NP+ ++CDEPVSALD+ Sbjct: 125 DERSRRTKELLDQVGLANAVKDRHTRELSGGQRQRVAIARSLAVNPRVLICDEPVSALDL 184 Query: 190 SIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPI 249 SI+AQ+++L +Q+ +G++ LFIAH+LA+V + +V VMYLGKIVE+G +++ P Sbjct: 185 SIRAQVMNLFLRLQKDLGVACLFIAHDLALVRQAASRVYVMYLGKIVEHGPSQQLYDRPS 244 Query: 250 HPYTRALLKSVPKIPWDGQKQRFYS---LKGELPSPIDLPKGCRFQTRCTEKKAICFEKE 306 HPYT+ LL SVP++ D + ++ S L GE+PSPI+ P GCRF+TRC C K Sbjct: 245 HPYTQMLLASVPEV--DPRVEKLRSGPLLMGEIPSPINPPSGCRFRTRCPLAVDECAGKA 302 Query: 307 PELTEVEKNHFVSC 320 P + +H +C Sbjct: 303 PPSHRLSPDHNAAC 316 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: 321 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 340 Length adjustment: 28 Effective length of query: 300 Effective length of database: 312 Effective search space: 93600 Effective search space used: 93600 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: 49 (23.5 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