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_05806 H281DRAFT_05806 dipeptide transport system ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_05806 Length = 339 Score = 269 bits (688), Expect = 6e-77 Identities = 131/292 (44%), Positives = 197/292 (67%), Gaps = 2/292 (0%) Query: 30 LKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEM 89 +KA++G+S ++ G+TL +VGESGCGKSTL R + + P G++ +G+D+ + ++ Sbjct: 40 VKALNGVSFALERGKTLAVVGESGCGKSTLARQLTMIEAPSAGRLLIDGEDVAGADHAKI 99 Query: 90 KPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGREF 149 R+++Q++FQ+P SLNP+ TV + + +PL I+ + ER +R+ +++ VG+ E Sbjct: 100 AALRRRVQMVFQNPFASLNPRKTVEQTLGEPLAINSQLSVTERAERIAQMMRTVGLRPEH 159 Query: 150 INSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGIS 209 +PH FSGGQ+QR+ IARA+ L+P+ +V DEPVSALDVSIQAQI++L ++QQ+ S Sbjct: 160 AKRYPHMFSGGQRQRVAIARAMILDPQIVVADEPVSALDVSIQAQILNLFMDLQQEFKTS 219 Query: 210 YLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIPWDGQK 269 Y+FI+HNL+VVEHI+ V VMY G + E GD +IF P HPYTRAL+ + P I ++ + Sbjct: 220 YVFISHNLSVVEHIADDVMVMYFGGVAELGDKKRIFSKPRHPYTRALMSATPSI-FEADR 278 Query: 270 QRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCH 321 L+GE+PSP++ P GC F RC C +EP+L EV+ VSCH Sbjct: 279 TIKIKLQGEMPSPLNPPSGCTFHQRCPYVIDRCRSEEPKLREVDGRQ-VSCH 329 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: 333 Number of extensions: 11 Number of successful extensions: 2 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: 339 Length adjustment: 28 Effective length of query: 300 Effective length of database: 311 Effective search space: 93300 Effective search space used: 93300 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