Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 8500263 DvMF_1020 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q9X271 (324 letters) >FitnessBrowser__Miya:8500263 Length = 358 Score = 283 bits (725), Expect = 3e-81 Identities = 157/337 (46%), Positives = 207/337 (61%), Gaps = 22/337 (6%) Query: 4 LLNVNNLKVEFH---RVEGI----VKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLR 56 LL+V +L VEF +G ++AV GIS+ + G +L +VGESG GKS++ L+LLR Sbjct: 17 LLDVRDLSVEFPGRPEADGTPGAPLRAVAGISFSIAPGGTLCLVGESGCGKSMTALALLR 76 Query: 57 LINRNGRIVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEP 116 L+ GR+ G G++LL L + E+R +RG+ IS+IFQ PMTSLNP+ RVG Q+ E Sbjct: 77 LVPEPGRVASGSVRLEGRELLTLPEPEMRGVRGRSISMIFQEPMTSLNPVFRVGEQIAEG 136 Query: 117 IIWHRLMKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLL 176 + H + +A RA++LL +VGIP R ++P Q SGGMRQRVMIAMALAC P+LL Sbjct: 137 VRLHLGLSRSDAAARAVDLLRQVGIPSPELRARDFPHQMSGGMRQRVMIAMALACDPRLL 196 Query: 177 IADEPTTALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEE 236 IADEPTTALDVTIQ QI+ L+++L G SV+ ITHDL V D + MYAG+I+E Sbjct: 197 IADEPTTALDVTIQRQILRLMRDLAAHRGASVLLITHDLGVVAETADHVAVMYAGRIMEH 256 Query: 237 APVEEILKTPLHPYTKGLLNSTLEI--GSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFA 294 A V + PLHPY +GL+ S + G R ++L IPG P PSGC F RC A Sbjct: 257 ASVGDFFARPLHPYAQGLMRSVPQAVSGPRAERLSAIPGTVPPLWALPSGCTFRDRCPHA 316 Query: 295 MEICQREEPPLV-------------NISENHRVACHL 318 C +EPPL+ N ++ H V C L Sbjct: 317 FARCAEQEPPLLAMPPQALAATPTDNAAQAHGVRCWL 353 Lambda K H 0.320 0.139 0.401 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: 307 Number of extensions: 12 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: 324 Length of database: 358 Length adjustment: 28 Effective length of query: 296 Effective length of database: 330 Effective search space: 97680 Effective search space used: 97680 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