Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate AO353_23195 AO353_23195 AP endonuclease
Query= reanno::Phaeo:GFF712 (297 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23195 Length = 307 Score = 226 bits (576), Expect = 5e-64 Identities = 112/307 (36%), Positives = 169/307 (55%), Gaps = 11/307 (3%) Query: 1 MTIRIGNAPCSWGVEFAQDPRNPDWRSVLKDCAEAGYKGIELGPVGYMPEDPAILRDALA 60 MT+ I APC WGV+ +P P W+ VL + A+AGY+GIELGP GY+P D A + LA Sbjct: 1 MTLHISTAPCCWGVDDVNNPHLPAWQQVLSEAAQAGYRGIELGPYGYLPLDAAAVGTVLA 60 Query: 61 EYDLELIGGVVFRAFHDPDQWDDVLDGAHRTCKAL-----------QAHGAQHLVLIDSI 109 E L ++ G VF DP +VL C L Q LV+ID Sbjct: 61 EQGLHVVAGTVFDNLVDPANLPNVLTQTRNICALLKQLPAVPQEPGQRFAMPCLVVIDWG 120 Query: 110 SPRRAPTAGRASEAEQMNHAEWSAFRDRLATVAQIGTEEYGLTVGIHAHAAGFMDFEPEL 169 R AG + A ++ W + + +A + E+G+ IH HA G+++F EL Sbjct: 121 HEERDYAAGHSERAPRLAPDAWRGMMNHIRAIADLAWLEFGVRTVIHPHAGGYIEFADEL 180 Query: 170 ERLLNEVDDKILKICFDTGHHSYAGFDPVAFMKRHMDRISYMHFKDIDPKVKADVIAKRT 229 +L+ ++ ++ +C DTGH YAG DPV ++++ DR+ Y+HFKDID V V+ + Sbjct: 181 AQLVADIPYEVAGLCLDTGHLYYAGMDPVQTLRQYADRLDYLHFKDIDQAVFDQVLGEHI 240 Query: 230 NFYDACGQGIFCNLGEGDVDFPAVRQLLVDTGFSGWCTVEQDCDPTLDPDPVGDARANRE 289 +F+ AC +G+ C +G+G +D+ A+R+L+ + G+ G+ TVEQ+ DP + D A+R Sbjct: 241 SFFGACARGVMCPIGQGVIDYRALRELITELGYQGYITVEQERDPRNARGSLRDVAASRA 300 Query: 290 YLESIGF 296 YL GF Sbjct: 301 YLSQAGF 307 Lambda K H 0.322 0.140 0.445 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: 294 Number of extensions: 20 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: 297 Length of database: 307 Length adjustment: 27 Effective length of query: 270 Effective length of database: 280 Effective search space: 75600 Effective search space used: 75600 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 (21.9 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