Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate HSERO_RS05315 HSERO_RS05315 LacI family transcriptional regulator
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__HerbieS:HSERO_RS05315 Length = 302 Score = 144 bits (362), Expect = 3e-39 Identities = 99/292 (33%), Positives = 157/292 (53%), Gaps = 10/292 (3%) Query: 12 AVALSATVSANAMAKDT----IALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNN 67 A+AL+ +A AMA++ I + +NNP+FVS+K + A LG ++ D+ +N Sbjct: 7 ALALTTLAAAPAMAQEVSKLKIGMSFQEMNNPYFVSMKKALDEAAKSLGAKVIATDAAHN 66 Query: 68 PAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIA 127 AK++A+++D+ + ILLINPTDS V AVK A N+ V+ +D A+ G V + Sbjct: 67 VAKQIADIEDMLQQNIDILLINPTDSAGVEAAVKAAKARNVIVVAVDANAS-GPVDMFVG 125 Query: 128 SDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHK-FNVLASQP 186 S N G + +A G +V L GI +R EG +QA+A +K ++A+Q Sbjct: 126 SKNKDAGYQSCRALADAIGGKGEVAILDGIP-VVPILQRVEGCKQALAEYKDIKLVATQN 184 Query: 187 ADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGE 246 DR L V++N++ + P+++ +F+ ND A+GAL A+Q +GK D+ + DG P+ Sbjct: 185 GRQDRSVALGVVENMIQSRPNLKGIFSVNDGGAMGALAAIQGSGK-DIKLTSVDGAPEAV 243 Query: 247 KAVND-GKLAATIAQLP-DQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ 296 KA+ D G T AQ P DQ+ K V + P+D+ V K+ Sbjct: 244 KAIADGGPFVETTAQFPRDQVRVGLAMALAKKWGARVVPKEVPIDVMPVTKK 295 Lambda K H 0.313 0.129 0.344 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: 215 Number of extensions: 12 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: 296 Length of database: 302 Length adjustment: 27 Effective length of query: 269 Effective length of database: 275 Effective search space: 73975 Effective search space used: 73975 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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