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 GFF3630 PGA1_262p00340 oligopeptide ABC transporter, ATP binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Phaeo:GFF3630 Length = 332 Score = 292 bits (747), Expect = 9e-84 Identities = 141/298 (47%), Positives = 207/298 (69%), Gaps = 1/298 (0%) Query: 25 QGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNL 84 Q R ++A++G+S+ +++GETLG+VGESGCGKSTL R I++L +P GG I G+DI Sbjct: 28 QPGRAVRALNGVSLALQKGETLGVVGESGCGKSTLARCIVRLYQPQGGSIRHHGQDIFAE 87 Query: 85 NDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVG 144 + + Y +++Q++FQDP SLNP+MT G+I+ + L +HK+ E RVEELL++V Sbjct: 88 GARRDRSYNRRVQMMFQDPYSSLNPRMTCGQILSEALHVHKMRPADEIPARVEELLELVR 147 Query: 145 IGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQ 204 + + PHEFSGGQ+QRI IARALA+ P+ ++ DE VSALDVS+QAQ+++LL E+Q+ Sbjct: 148 LPADAAQKLPHEFSGGQRQRIAIARALAVEPEVLIADELVSALDVSVQAQVVNLLLELQE 207 Query: 205 KMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKIP 264 ++ ++ LF+AH+L +V H+SH+VAV+YLG+IVE GD + +F NP HPY++ALL + P + Sbjct: 208 QLDLTILFVAHDLRLVRHVSHRVAVIYLGRIVEIGDSETLFANPAHPYSQALLSAAPSLD 267 Query: 265 WDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSCHL 322 D L+GELPSP+++P GC F RC +C P L + V+CHL Sbjct: 268 PDDTGDAI-RLEGELPSPLNVPPGCPFHVRCAHAADVCRRDVPRLRPLGDRGEVACHL 324 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: 352 Number of extensions: 16 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: 332 Length adjustment: 28 Effective length of query: 300 Effective length of database: 304 Effective search space: 91200 Effective search space used: 91200 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