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 Ac3H11_2051 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2051 Length = 348 Score = 233 bits (593), Expect = 7e-66 Identities = 131/304 (43%), Positives = 182/304 (59%), Gaps = 9/304 (2%) Query: 13 LLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG- 71 LL+ +L FP + L+A+D IS I GE LG+VGESG GKS G I+ LL P G Sbjct: 14 LLEVKNLVVEFPGRRGTLRALDDISFSIAPGEILGVVGESGAGKSLTGAAIIGLLEPPGR 73 Query: 72 ---GKIFFEGKDITNLNDKEMKPYR-KKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127 G+I EG+ I NL+++EM+ R +++ IFQDPL SLNP TVGR + + ++ H Sbjct: 74 VASGQILLEGQRIDNLSNEEMRHIRGRRIGAIFQDPLTSLNPLYTVGRQLTETILAHLPV 133 Query: 128 TKKERRKRVEELLDMVGI--GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVS 185 T E R+R LL GI E I+ +PH+FSGG +QR+ IA ALA PK IV DEP + Sbjct: 134 TPAEARQRAIALLKDTGIPAAEERIDHYPHQFSGGMRQRVVIALALAAEPKLIVADEPTT 193 Query: 186 ALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245 ALDVSIQAQII LL+ I + G + + I H++ V+ +VAV+Y G++ E G V + Sbjct: 194 ALDVSIQAQIITLLKNICKSRGAAVMLITHDMGVIAETCDRVAVLYAGRVAEIGPVHDVI 253 Query: 246 LNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEK 305 P HPYT L+ S+P + D ++R + G +P +PKGC + RC + C + Sbjct: 254 NKPSHPYTSGLMASIPDMTMD--RERLNQIDGAMPRLNAIPKGCAYNPRCPQTFDRCMTE 311 Query: 306 EPEL 309 P+L Sbjct: 312 RPDL 315 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: 305 Number of extensions: 17 Number of successful extensions: 5 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: 348 Length adjustment: 28 Effective length of query: 300 Effective length of database: 320 Effective search space: 96000 Effective search space used: 96000 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