Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate WP_053939460.1 WG78_RS19225 SMP-30/gluconolactonase/LRE family protein
Query= reanno::BFirm:BPHYT_RS16915 (300 letters) >NCBI__GCF_001294205.1:WP_053939460.1 Length = 301 Score = 235 bits (599), Expect = 1e-66 Identities = 131/281 (46%), Positives = 165/281 (58%), Gaps = 4/281 (1%) Query: 20 LGEGATWCAQTGHFYWTDIEGARLWRYDPRDCSNMSWHMPERLATFALCADPRYLLLGLA 79 L EG Q+G +WT+I LW+ D R + W P+R+ FA D LL+ Sbjct: 20 LAEGIIQHPQSGLLWWTNIHAKELWQLDLRTGQHRYWSTPQRVCCFAFTQDDDVLLVAFD 79 Query: 80 THLAFFELATGETRRIIDVEAGL-NTRVNDGRCDRQGRFVFGTKDEGAPLQAIGGFYRLG 138 LA F A+G +R+ VE TR NDGR DR G VFGT E + +A G FYR Sbjct: 80 AGLALFNTASGAIKRLTPVEPETPGTRCNDGRVDRAGNLVFGTMHERSA-EAKGHFYRFD 138 Query: 139 HDLSLERLPLPAPAISNSIAFSPDGATMYYCDSPTREIRACDYRA-DGSIANDRLFTRLT 197 + L++L LPA AISNS+AFSPDG T+Y+CDS +I C Y + G+IA +F L Sbjct: 139 TESRLQQLALPAIAISNSLAFSPDGGTLYWCDSLQHKIMQCAYDSVTGAIAEISVFHDLG 198 Query: 198 DATGEPDGSTVDRDGGLWNAQWGGRRVVRYGPDGMETERVDVPTAQPSCVALGGTQLDTL 257 D EPDGSTVD G LWNA+W G V RY PDG ++ +P AQP+CV GG + +TL Sbjct: 199 DTVIEPDGSTVDAAGYLWNAEWAGHCVTRYAPDGSIDRKIHLPVAQPTCVTFGGPEQNTL 258 Query: 258 YITSARCDLDAAALANDPHAGGVFIATL-GRRGLPEPVFQG 297 +ITSAR LD AALA P AG VF + G RGLPE ++ G Sbjct: 259 FITSARAGLDDAALAQQPEAGSVFALEIPGVRGLPENIWLG 299 Lambda K H 0.321 0.138 0.443 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: 317 Number of extensions: 22 Number of successful extensions: 4 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: 300 Length of database: 301 Length adjustment: 27 Effective length of query: 273 Effective length of database: 274 Effective search space: 74802 Effective search space used: 74802 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: 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