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 17601 b3540 dipeptide transporter (NCBI)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Keio:17601 Length = 334 Score = 311 bits (796), Expect = 2e-89 Identities = 149/319 (46%), Positives = 230/319 (72%), Gaps = 8/319 (2%) Query: 11 KPLLQTVDLKKYFPQGK------RILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64 +PLLQ +DLKK++P K R++KA+DG+S ++ G+TL +VGESGCGKSTLGR + Sbjct: 10 QPLLQAIDLKKHYPVKKGMFAPERLVKALDGVSFNLERGKTLAVVGESGCGKSTLGRLLT 69 Query: 65 KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 + P GG+++++G+D+ + + K R+K+QI+FQ+P GSLNP+ VG+I+E+PL+I+ Sbjct: 70 MIEMPTGGELYYQGQDLLKHDPQAQKLRRQKIQIVFQNPYGSLNPRKKVGQILEEPLLIN 129 Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 +K++RR++ ++ VG+ E + +PH FSGGQ+QRI IAR L L+P ++ DEPV Sbjct: 130 TSLSKEQRREKALSMMAKVGLKTEHYDRYPHMFSGGQRQRIAIARGLMLDPDVVIADEPV 189 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALDVS++AQ+++L+ ++QQ++G+SY+FI+H+L+VVEHI+ +V VMYLG+ VE G D+I Sbjct: 190 SALDVSVRAQVLNLMMDLQQELGLSYVFISHDLSVVEHIADEVMVMYLGRCVEKGTKDQI 249 Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFE 304 F NP HPYT+ALL + P++ D +++R L GELPSP++ P GC F RC + C + Sbjct: 250 FNNPRHPYTQALLSATPRLNPDDRRERI-KLSGELPSPLNPPPGCAFNARCRRRFGPCTQ 308 Query: 305 KEPELTEVEKNHFVSCHLV 323 +P+L + V+C V Sbjct: 309 LQPQLKDY-GGQLVACFAV 326 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: 384 Number of extensions: 19 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: 334 Length adjustment: 28 Effective length of query: 300 Effective length of database: 306 Effective search space: 91800 Effective search space used: 91800 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