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 H281DRAFT_03125 H281DRAFT_03125 oligopeptide transport system ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_03125 Length = 332 Score = 271 bits (693), Expect = 2e-77 Identities = 137/285 (48%), Positives = 199/285 (69%), Gaps = 8/285 (2%) Query: 26 GKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLN 85 GK L+AVDG+S ++ GET+GLVGESGCGKSTL R I+ L G + + G N Sbjct: 35 GKTTLRAVDGVSFNVRRGETIGLVGESGCGKSTLARAIIGLAPVASGSVRWLG------N 88 Query: 86 DKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH-KIGTKKERRKRVEELLDMVG 144 + + R+ +Q+IFQDPL SL+P+MT+ +I+ +PL+ H K + + ++RV +L+ VG Sbjct: 89 ETVLPNARRDVQMIFQDPLASLDPRMTIEQIVAEPLLTHGKDIARADVQRRVLTMLERVG 148 Query: 145 IGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQ 204 + + + +PHEFSGGQ QR+GIARAL P+ ++CDEPVSALDVSIQAQI++LL ++Q+ Sbjct: 149 LNAQHLRRYPHEFSGGQCQRVGIARALIGEPQLVICDEPVSALDVSIQAQIVNLLRDLQR 208 Query: 205 KMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVP-KI 263 ++ +S LF+AH+LAVV+ ISH+V VMYLG+++E+GD ++ P HPYTRALL +VP Sbjct: 209 ELSLSLLFVAHDLAVVKAISHRVLVMYLGRVMEFGDKRDVYGTPRHPYTRALLSAVPVPD 268 Query: 264 PWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPE 308 P + +R L+GE+ SP+ P GC F+TRC + C + P+ Sbjct: 269 PAIERARRHLLLRGEIASPLSPPSGCAFRTRCPDAIDACAAQIPQ 313 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: 314 Number of extensions: 9 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: 332 Length adjustment: 28 Effective length of query: 300 Effective length of database: 304 Effective search space: 91200 Effective search space used: 91200 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