Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate AZOBR_RS02620 AZOBR_RS02620 D-ala-D-ala transporter subunit
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__azobra:AZOBR_RS02620 Length = 306 Score = 190 bits (483), Expect = 3e-53 Identities = 98/272 (36%), Positives = 151/272 (55%), Gaps = 2/272 (0%) Query: 17 WLRFKKNKMAVIGGVFVLILIALAILAPYIAPY-PYDEPHYIRAFEGPSKDFIFGTDALG 75 WL F +N++A+IG VL+L+ +A LAP +APY PY + R PS GTDA G Sbjct: 36 WLAFARNRLAMIGLGIVLLLVLMAALAPLLAPYDPYTQDLSQRLLP-PSAAHWLGTDAFG 94 Query: 76 RDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTF 135 RD+ SRILY R +I + G ++G VAG+ GGW+D +M + DI AFP Sbjct: 95 RDILSRILYGSRLTLMIVALVAVTAPVAGLLIGTVAGYLGGWVDAVLMRVTDIFLAFPKL 154 Query: 136 LFNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYII 195 + + V+ALG G+ +AI +T W AR+ R + + ++ S+F+ AA+ GAST II Sbjct: 155 ILALAFVSALGPGIENAIIAIAITSWPPYARIARAETITIRKSDFISAARLQGASTPRII 214 Query: 196 RKHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPH 255 H++P ++V + + G ++T +GL +G+G +PP P WG +I G ++ Sbjct: 215 LGHVVPLCSSSLIVRVTLDMAGIILTAAGLGFLGLGAQPPAPEWGAMIATGRQYVLEQWW 274 Query: 256 LLIFPAVTFAFTLISFTFLADGLRDAFNPRSE 287 + P + + F L DGLRD +P+ + Sbjct: 275 VATMPGIAIFVVSLGFNLLGDGLRDVLDPKGQ 306 Lambda K H 0.331 0.147 0.457 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: 232 Number of extensions: 16 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: 289 Length of database: 306 Length adjustment: 26 Effective length of query: 263 Effective length of database: 280 Effective search space: 73640 Effective search space used: 73640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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