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_694 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_694 Length = 341 Score = 293 bits (750), Expect = 4e-84 Identities = 144/313 (46%), Positives = 213/313 (68%), Gaps = 5/313 (1%) Query: 12 PLLQTVDLKKYFPQGKRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDG 71 PLL+ L+K+F G ++AVD +S I GETLGLVGESG GKST+GR + +L+ P Sbjct: 19 PLLEIAHLRKHFGSGPHPVRAVDDVSFTIHRGETLGLVGESGSGKSTIGRLLTRLVDPTS 78 Query: 72 GKIFFEG----KDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIG 127 G++ + G +D+ L+ + +P R ++QIIFQDP SLNP+M + ++ + L H + Sbjct: 79 GQMRYHGGAAPQDLAQLSQSQYRPLRSQIQIIFQDPYASLNPRMRIRDVLAEALDTHGLA 138 Query: 128 TKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSAL 187 R R+ +LL+ VG+ E FPHEFSGGQ+QRIGIARALA+ P+FIV DEP+SAL Sbjct: 139 KGAARLPRIHQLLEQVGLRPEHAERFPHEFSGGQRQRIGIARALAVEPQFIVADEPLSAL 198 Query: 188 DVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLN 247 DVSIQAQ+++LL E+++++G++ LFI+H+L VVE++ +V V+YLG+++E + ++ Sbjct: 199 DVSIQAQVVNLLGELKEQLGLTLLFISHDLDVVEYLCDRVVVLYLGRVMEIAPTEALYAQ 258 Query: 248 PIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEP 307 P HPYT+ALL + P IP Q++ L+G+LPSP + P GC F+TRC + +A C + Sbjct: 259 PQHPYTQALLAAAP-IPDPAQRRSIALLQGDLPSPANPPSGCVFRTRCPQAEARCASADM 317 Query: 308 ELTEVEKNHFVSC 320 +L EV H +C Sbjct: 318 QLREVAPGHLHAC 330 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: 340 Number of extensions: 15 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: 328 Length of database: 341 Length adjustment: 28 Effective length of query: 300 Effective length of database: 313 Effective search space: 93900 Effective search space used: 93900 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