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 AZOBR_RS26740 AZOBR_RS26740 peptide ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__azobra:AZOBR_RS26740 Length = 315 Score = 242 bits (618), Expect = 8e-69 Identities = 131/314 (41%), Positives = 192/314 (61%), Gaps = 7/314 (2%) Query: 12 PLLQTVDLKKYFP-QGKR--ILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLR 68 PL + + + FP G R +L+AVDG+ + ++ GE +GLVGESGCGKST+ R LL Sbjct: 4 PLAELRGVSRLFPIPGWRGAVLRAVDGVDLAVRRGELVGLVGESGCGKSTVARIATGLLP 63 Query: 69 PDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGT 128 P G++ +G+D E + R ++Q++FQ+P SLNP+ TV I+ + + H++ Sbjct: 64 PSAGRVLIDGQDAAERPAAEARAARLRVQMVFQNPHASLNPRFTVEEIVGEAVRHHRLVP 123 Query: 129 KKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALD 188 + + V L VG+ + PH FSGGQ+QRIGIARALA+ P +VCDEPV+ALD Sbjct: 124 RAALAEHVAAQLLRVGLDPALRHHHPHRFSGGQRQRIGIARALAVRPDLLVCDEPVTALD 183 Query: 189 VSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNP 248 VS++A I++L +++ + G++ LFI+H+L+VV HI +V VMYLG++VE G VD +F P Sbjct: 184 VSVRAGILNLFLDLRDRDGLAILFISHDLSVVGHICDRVVVMYLGRVVEEGPVDALFERP 243 Query: 249 IHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPE 308 HPYT+ALL +G ++GE PS + P GC F RC + C + P Sbjct: 244 RHPYTQALLADSRSALPEGT----VPVRGEAPSLAERPAGCPFHPRCPMARPDCRREVPV 299 Query: 309 LTEVEKNHFVSCHL 322 L V + H V+C L Sbjct: 300 LRGVGEGHRVACLL 313 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: 293 Number of extensions: 14 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: 315 Length adjustment: 28 Effective length of query: 300 Effective length of database: 287 Effective search space: 86100 Effective search space used: 86100 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