Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate WP_053939460.1 WG78_RS19225 SMP-30/gluconolactonase/LRE family protein
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >NCBI__GCF_001294205.1:WP_053939460.1 Length = 301 Score = 278 bits (712), Expect = 8e-80 Identities = 135/286 (47%), Positives = 188/286 (65%), Gaps = 2/286 (0%) Query: 3 VQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFTA 62 +Q L G + L EG++ +S ++WT+IHA LW D +TG R W P+R+CC+AFT Sbjct: 10 LQSLSAGQYNLAEGIIQHPQSGLLWWTNIHAKELWQLDLRTGQHRYWSTPQRVCCFAFTQ 69 Query: 63 DPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDAGR 122 D LL+ ++ LA FN ++G I + +E + P TR NDGR DR G VFGT++E + Sbjct: 70 DDDVLLVAFDAGLALFNTASGAIKRLTPVEPETPGTRCNDGRVDRAGNLVFGTMHERSAE 129 Query: 123 APIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASGAV 182 A FYR +T+ L++L+LP+IAISNS+ FS DG +Y CDS+ KIM C YD+ +GA+ Sbjct: 130 AK-GHFYRFDTESRLQQLALPAIAISNSLAFSPDGGTLYWCDSLQHKIMQCAYDSVTGAI 188 Query: 183 GGQRVFADVAQPG-GPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQPSCV 241 VF D+ PDGST+DA GYLWNA+W G V RYAPDG IDR + +P +QP+CV Sbjct: 189 AEISVFHDLGDTVIEPDGSTVDAAGYLWNAEWAGHCVTRYAPDGSIDRKIHLPVAQPTCV 248 Query: 242 AFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPE 287 FGG + +TL++T+A G+ A P+AG++FA+ + VRGLPE Sbjct: 249 TFGGPEQNTLFITSARAGLDDAALAQQPEAGSVFALEIPGVRGLPE 294 Lambda K H 0.322 0.138 0.437 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: 373 Number of extensions: 24 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: 292 Length of database: 301 Length adjustment: 26 Effective length of query: 266 Effective length of database: 275 Effective search space: 73150 Effective search space used: 73150 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 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