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 GFF666 PGA1_c06800 dipeptide transport system permease protein DppC
Query= TCDB::Q9X270 (289 letters) >FitnessBrowser__Phaeo:GFF666 Length = 304 Score = 181 bits (459), Expect = 2e-50 Identities = 107/302 (35%), Positives = 166/302 (54%), Gaps = 24/302 (7%) Query: 6 KTESIGYWKAFWLRFKKNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSK 65 K ++I + W F+ + +AV+ + VL+L ILAP IAP+ +P + G SK Sbjct: 3 KLKNIWHSDLAW-NFRNSPVAVVSALIVLVLALAVILAPLIAPHNPFDPATLNLMNGFSK 61 Query: 66 D----------FIFGTDALGRDLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKG 115 F+ GTD GRD+FS ILY +R + ++G S +++G ILG +AG+ G Sbjct: 62 PMHPNEFTGEVFLLGTDDQGRDVFSTILYGMRISLMVGVLSVTFAMVLGIILGLLAGYVG 121 Query: 116 GWIDKFIMSIVDIMFAFPTFLFNVILVTALGRG-----------LFTIFLAIGLTGWAGM 164 GW + IM + D+ FP+ L +L+ + +G ++ + LAIGL W Sbjct: 122 GWTETIIMRVADVQLTFPSILV-AMLIFGIVKGVTPVEYRDQMAIWVLILAIGLGEWVQF 180 Query: 165 ARLVRGQVLYLKNSEFVEAAKAAGASTFYIIRKHILPNMIGPILVNLAFGVPGAMMTESG 224 AR+VRG L KN E+V+AA+ G S + I+ +H+LPN++ P+LV + A++ E+ Sbjct: 181 ARVVRGATLVEKNREYVQAARLIGRSKWVIMIRHLLPNVLSPVLVIATISLALAIIAEAT 240 Query: 225 LAVIGMGVRPPMPSWGNLIGEGIGMMMAFP-HLLIFPAVTFAFTLISFTFLADGLRDAFN 283 L+ +G+G P PS G LI G G + + +L+FPA+T +S L D LRDA N Sbjct: 241 LSFLGVGAPPTQPSLGTLIRIGQGFLFSGEWWILLFPALTLLTLALSVNMLGDWLRDALN 300 Query: 284 PR 285 P+ Sbjct: 301 PK 302 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: 233 Number of extensions: 8 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: 304 Length adjustment: 26 Effective length of query: 263 Effective length of database: 278 Effective search space: 73114 Effective search space used: 73114 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