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 15604 b1483 D-ala-D-ala transporter subunit (NCBI)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Keio:15604 Length = 308 Score = 246 bits (628), Expect = 5e-70 Identities = 135/291 (46%), Positives = 188/291 (64%), Gaps = 23/291 (7%) Query: 13 LLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTILK 65 LL D+ FP K L A++GI ++I+ GETLG+VGESGCGKSTL + ++ Sbjct: 5 LLTLRDVHINFPARKNWLGKTTEHVHAINGIDLQIRRGETLGIVGESGCGKSTLAQLLMG 64 Query: 66 LLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHK 125 +L+P G+ G ++ MQ++FQDPL SLNP++ V RII +PL I K Sbjct: 65 MLQPSHGQYIRSGS-------------QRIMQMVFQDPLSSLNPRLPVWRIITEPLWIAK 111 Query: 126 IGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVS 185 ++++RR EEL VGI E+++ PH FSGGQ+QRI IARAL+ P IV DEP S Sbjct: 112 RSSEQQRRALAEELAVQVGIRPEYLDRLPHAFSGGQRQRIAIARALSSQPDVIVLDEPTS 171 Query: 186 ALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245 ALD+S+QAQI++LL +Q+ G++Y+ I+HN++V+ H+S +VAVMYLG+IVE GD ++ Sbjct: 172 ALDISVQAQILNLLVTLQENHGLTYVLISHNVSVIRHMSDRVAVMYLGQIVELGDAQQVL 231 Query: 246 LNPIHPYTRALLKSVPKIPWDGQKQRFYSL-KGELPSPIDLPKGCRFQTRC 295 P HPYTR LL S+P I D + ++L K +LP LP+GC F RC Sbjct: 232 TAPAHPYTRLLLDSLPAI--DKPLEEEWALRKTDLPGNRTLPQGCFFYERC 280 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: 283 Number of extensions: 12 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: 308 Length adjustment: 27 Effective length of query: 301 Effective length of database: 281 Effective search space: 84581 Effective search space used: 84581 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: 48 (23.1 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