Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate CCNA_01882 CCNA_01882 SMP-30/gluconolaconase/LRE-like protein
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__Caulo:CCNA_01882 Length = 293 Score = 169 bits (427), Expect = 9e-47 Identities = 104/288 (36%), Positives = 141/288 (48%), Gaps = 3/288 (1%) Query: 3 VQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFTA 62 V+++ LGE LW + ++W D A +W +DP T RS P+ + Sbjct: 5 VEIIGKERCRLGESPLWDADAGVLYWVDSMAPAIWRYDPFTSEQRSIPAPKPIGSVVL-G 63 Query: 63 DPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDAGR 122 P +L+ GL + L TG PI + P R NDG+ DRQGRFV GT+ Sbjct: 64 RPGELIAGLADGVYRVQLDTGAFTPIALPDTLAPIERFNDGKADRQGRFVTGTMAMHNET 123 Query: 123 APIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASGAV 182 I YR + E L I I+NS CFS G +Y DS+ + YD +GAV Sbjct: 124 GRIGKLYRFSAGGAWEVLPTEPIEIANSTCFSPSGDTLYFADSLRHMVWAFSYDPKTGAV 183 Query: 183 GGQRVFADVAQ-PGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQPSCV 241 G +R F D PDG+T+DAEG++W A +++R +PDGR+DRVV P SC Sbjct: 184 GEKRDFFDTTGFNSAPDGATVDAEGHIWLALVQAQKLIRISPDGRLDRVVESPAPFCSCP 243 Query: 242 AFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVR 289 AFGG D LYVT+ + + D +G L A VRG+ E R Sbjct: 244 AFGGEDLDILYVTSISDSGGRLKTDVD-ASGRLMAFHGLGVRGIAETR 290 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: 311 Number of extensions: 20 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: 293 Length adjustment: 26 Effective length of query: 266 Effective length of database: 267 Effective search space: 71022 Effective search space used: 71022 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