Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate Ac3H11_700 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
Query= reanno::Cup4G11:RR42_RS28860 (311 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_700 Length = 319 Score = 296 bits (759), Expect = 3e-85 Identities = 162/308 (52%), Positives = 198/308 (64%), Gaps = 10/308 (3%) Query: 4 DILAFGEALVEFNQQPDDPSRYLQGFGGDTSNFCIAAARQGARAGYISAVGEDTFGERLL 63 D++A GEALVEFNQ +YLQGFGGDTSN IAAAR GAR Y++ +G D FG+ LL Sbjct: 10 DVVALGEALVEFNQTRPGEPQYLQGFGGDTSNAVIAAARAGARTAYLTRLGSDAFGQALL 69 Query: 64 ALWTQERVDTRHVRIDAGAPTGVYFVTHDAHGHRFDYLRSGSAASHYSHENL-------P 116 LW +E VDT V DA PTG+YFVTH A GH F YLR+GSAAS + L P Sbjct: 70 DLWAREGVDTTAVERDAQHPTGIYFVTHGAAGHEFSYLRAGSAASRMAPAWLADESVKGP 129 Query: 117 HHAIAEARYLHVSGISLAISTSACDAGLAAMEHARKAGCQVTLDTNLRLRLWTLARARGI 176 + + R LHVSGISLA+S SACD AM AR AG +V D NLRL+LW LARAR Sbjct: 130 AAVLQQCRILHVSGISLAVSASACDTAYEAMRVARAAGARVAFDPNLRLKLWPLARARAC 189 Query: 177 MREAFALTDVCLPSWDDITVLTGLDDRDAIVDYLLGCGIGLVALKLGEEGAYVATPE--- 233 + A +L D+ LP DD+ L GL D DAI D+ G V +KLG +G +++ + Sbjct: 190 IAHAVSLCDIFLPGLDDMAALLGLSDADAIADWGHAQGAATVVVKLGADGVLLSSADPAV 249 Query: 234 ARTLVPPYTVRPVDATGAGDCFGGSFVARLAAGDDPFDAARYANVAAALSTTGYGAVAPI 293 R VP +V VDATGAGDCF G+ +ARLA GDD A RYAN AA+L+ G+GAVAP+ Sbjct: 250 PRQRVPGRSVALVDATGAGDCFDGNLLARLALGDDLAAAVRYANTAASLAVQGFGAVAPL 309 Query: 294 PSIETVLA 301 P+ + V A Sbjct: 310 PTAQQVQA 317 Lambda K H 0.321 0.136 0.409 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: 11 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: 311 Length of database: 319 Length adjustment: 27 Effective length of query: 284 Effective length of database: 292 Effective search space: 82928 Effective search space used: 82928 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