Align Putative sugar lactone lactonase; EC 3.1.1.- (characterized, see rationale)
to candidate WP_012334362.1 M446_RS22215 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:Q92RN9 (294 letters) >NCBI__GCF_000019365.1:WP_012334362.1 Length = 335 Score = 255 bits (651), Expect = 1e-72 Identities = 139/318 (43%), Positives = 180/318 (56%), Gaps = 33/318 (10%) Query: 8 SGRTLSEAASELGEGPTFDPGTGTAWWFNITGRELHELH--------------------- 46 + R LGEG T++ TGTAWWF+I R L E Sbjct: 17 AARVFDATPCHLGEGVTYEAETGTAWWFDILSRRLFEARGLSEARGLSEARGLSDVPDPP 76 Query: 47 -----LESGRKA----IHPLPFLGSVLAVIDPLRQLIASDQGLFVRDTESSKLGHFATLE 97 L++G +H LP + S LA + R ++A++ GL +R + +L A +E Sbjct: 77 DASRPLDAGPTGGDVRVHSLPVMASALAAVGDGRHVLAAEDGLHLRAPDG-RLTLLAPVE 135 Query: 98 -EKPGNRSNDGRIHPCGALWIGTMGRSAEKHAGAIYHVAGSRVTKLYSNITIPNAICFSP 156 + P RSND R+HP G W TMGR AE AGAIY RV +L+S + IPNAICFSP Sbjct: 136 ADDPRTRSNDARVHPSGTFWFSTMGREAEPGAGAIYAFQAGRVLRLFSGLRIPNAICFSP 195 Query: 157 DGATAYFTDTDVNQLMRVDIDPATALPTGDPVLLSDESTSPGGVDGAVCDADGLIWNARW 216 DG+ YF DT +L RV +D AT LP G P L+ P G+DGAV DA G +W ARW Sbjct: 196 DGSAGYFADTGAGELHRVPLDAATGLPEGAPALVLRHD-DPAGLDGAVTDAQGCLWIARW 254 Query: 217 GASAVEVYKPDGQKVARYAVPATQPSCPAFVGAKAERLLVTSAWQGMDDAARAADPHAGK 276 G + V+ + P G + A+PA QPSCPAFVGA+ +RLLVTSA+QG+D AARAADP G+ Sbjct: 255 GGARVDAFSPQGTLLRSVAIPALQPSCPAFVGARLDRLLVTSAFQGLDAAARAADPLGGQ 314 Query: 277 TFELGIEVKGRFEPAFRL 294 TF + +G+ EP RL Sbjct: 315 TFLVAPGARGKPEPRIRL 332 Lambda K H 0.317 0.135 0.418 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: 356 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 294 Length of database: 335 Length adjustment: 27 Effective length of query: 267 Effective length of database: 308 Effective search space: 82236 Effective search space used: 82236 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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