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 WP_086509536.1 BZY95_RS08635 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >NCBI__GCF_002151265.1:WP_086509536.1 Length = 348 Score = 283 bits (725), Expect = 3e-81 Identities = 150/331 (45%), Positives = 211/331 (63%), Gaps = 18/331 (5%) Query: 13 LLQTVDLKKYFPQGKR------------ILKAVDGISIEIKEGETLGLVGESGCGKSTLG 60 LL+ DL +YF K LKAVDG+ I+ GETL LVGESGCGKST+ Sbjct: 18 LLEAQDLARYFDVSKPWLNRVIERSEKLTLKAVDGVGFSIRRGETLSLVGESGCGKSTVA 77 Query: 61 RTILKLLRPDGGKIFFEGKDITNL---NDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRII 117 R ++ L GK+ F+G+DI++L ++ RK+ Q+IFQDP SLNP VG II Sbjct: 78 RLVVGLYGLTRGKLVFDGEDISDLAGRTGRQAASVRKRFQMIFQDPYASLNPLWRVGTII 137 Query: 118 EDPLIIHKIG-TKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPK 176 +PL + + +RR+RV ELL+ VG+ N +PHEFSGGQ+QRI IARALA P+ Sbjct: 138 GEPLRFFRPEMSSADRRRRVGELLEQVGMSAMDANRYPHEFSGGQRQRISIARALANEPE 197 Query: 177 FIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIV 236 F++CDEP SALDVS+QAQI++L+ ++Q + G++YLFI+H++AVV+H+S ++AVMYLG+I Sbjct: 198 FMICDEPTSALDVSVQAQILNLMRDLQDEFGLTYLFISHDMAVVKHMSDRIAVMYLGRIA 257 Query: 237 EYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCT 296 E D++F NP HPY++ LL +VP + G+++ ++GE+P+P+ P GC F RC Sbjct: 258 EIAPADQLFENPHHPYSKMLLAAVPSLEGVGKERTV--IQGEVPNPVHPPTGCAFHPRCP 315 Query: 297 EKKAICFEKEPELTEVEKNHFVSCHLVRSYR 327 C + P L V+CH V R Sbjct: 316 HANERCKAEVPRLIARSDGSEVACHGVEEGR 346 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: 355 Number of extensions: 12 Number of successful extensions: 4 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: 348 Length adjustment: 28 Effective length of query: 300 Effective length of database: 320 Effective search space: 96000 Effective search space used: 96000 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 24 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