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 HSERO_RS07885 HSERO_RS07885 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__HerbieS:HSERO_RS07885 Length = 335 Score = 264 bits (675), Expect = 2e-75 Identities = 130/294 (44%), Positives = 198/294 (67%), Gaps = 3/294 (1%) Query: 29 ILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKE 88 I A+D + +++ GE +GLVGESGCGKSTLGR LL P G++ G+D +L+ +E Sbjct: 41 ITHALDKVDLKVLPGEVVGLVGESGCGKSTLGRVACGLLDPSDGQVLVNGRDRASLSSRE 100 Query: 89 MKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGRE 148 R ++Q+IFQ+P SLNP++ + +I+ + ++ + + V + L G+ Sbjct: 101 EAEARLQVQMIFQNPYASLNPRLRIDQIVGEAAQVNG-KVEGDLDDYVCQQLLRAGLDPA 159 Query: 149 FINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGI 208 + +PH+FSGGQ+QRIGIARALA+ P+ +VCDE V+ALDVSIQAQI++L +++ ++G+ Sbjct: 160 LRDRYPHQFSGGQRQRIGIARALAVQPQMLVCDEAVAALDVSIQAQILNLFMDLRAELGL 219 Query: 209 SYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQ 268 +YLFI+H+L VVEH+S +V +MYLG++VE V ++F P HPYT+ALL VP++ + Sbjct: 220 TYLFISHDLGVVEHVSDRVVIMYLGRVVESAPVAELFGQPNHPYTQALLAEVPRM--GAR 277 Query: 269 KQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHL 322 K+ F ++KGE+PSP++ P GC F RC C E++P L E+ H +CHL Sbjct: 278 KKEFTAIKGEIPSPLNPPTGCHFNPRCPHATQRCREEQPLLREIAPGHMSACHL 331 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: 354 Number of extensions: 14 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: 335 Length adjustment: 28 Effective length of query: 300 Effective length of database: 307 Effective search space: 92100 Effective search space used: 92100 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