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 AO356_29390 AO356_29390 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29390 Length = 329 Score = 276 bits (707), Expect = 4e-79 Identities = 150/310 (48%), Positives = 203/310 (65%), Gaps = 17/310 (5%) Query: 19 LKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEG 78 + K F + ILKAVDG+S+ + GETLGLVGESGCGKSTL + +L LL P G + G Sbjct: 18 INKGFFKPAAILKAVDGVSLRLMRGETLGLVGESGCGKSTLAKLLLGLLAPTSGDVLVNG 77 Query: 79 KDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEE 138 K + + KEM + +Q IFQDP SLNP+ T+ II PLI+H IG+ ERRK+ E Sbjct: 78 KHLAATDRKEMA---RHIQPIFQDPYSSLNPRKTLRDIITLPLIVHDIGSPAERRKKTEA 134 Query: 139 LLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDL 198 +LD+VG+ + I+S+P + SGGQ+QR+ IARAL + P ++CDEP SALDVS+QAQI++L Sbjct: 135 MLDVVGLPKRVIDSYPSQLSGGQRQRVAIARALIMRPDVLICDEPTSALDVSVQAQILNL 194 Query: 199 LEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLK 258 L++++++ G++YL I+HNLAV+EH++ +VAVMYLG+IVE + +F P HPYTRALL Sbjct: 195 LQDLKREFGLTYLLISHNLAVIEHLADRVAVMYLGRIVEERTRESLFAEPGHPYTRALLD 254 Query: 259 SV----PK--IPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEV 312 SV P+ IP G L G P+P+ P GC F RC A C P + Sbjct: 255 SVLTPDPRLGIPEIG-------LHGTFPNPMSPPSGCAFHPRCPSCFAPCKTAYPANDPI 307 Query: 313 EKNHFVSCHL 322 + V CHL Sbjct: 308 IGGN-VRCHL 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: 323 Number of extensions: 9 Number of successful extensions: 3 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: 329 Length adjustment: 28 Effective length of query: 300 Effective length of database: 301 Effective search space: 90300 Effective search space used: 90300 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