Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate BWI76_RS23720 BWI76_RS23720 calcium-binding protein
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__Koxy:BWI76_RS23720 Length = 292 Score = 192 bits (489), Expect = 6e-54 Identities = 103/294 (35%), Positives = 169/294 (57%), Gaps = 4/294 (1%) Query: 1 MNVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAF 60 M +++L+D LGE +W Q ++W D RL+ + Q G +SW + +++ +A Sbjct: 1 MRIEVLLDLKTRLGESPVWDIEQQRLWWVDSLDGRLFACNAQGGAIKSWDVRQKIGSFAL 60 Query: 61 TADPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDA 120 + + ++ L++ + + ++G + + E D P RLNDG+ DRQGRF+FG++ + Sbjct: 61 RQNGEGAVVALQNGVHLLDFASGGLTLLHHPEADRPFNRLNDGKVDRQGRFLFGSM-DMR 119 Query: 121 GRAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASG 180 P + YRL+ DL+L L +I +SN+ C+S G+ Y D+ G+I DY+TA+G Sbjct: 120 EEEPSGALYRLDADLSLHVLK-KNIIVSNAPCWSPSGETFYFADTWTGEICAWDYNTATG 178 Query: 181 AVGGQRVF--ADVAQPGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQP 238 + G+RVF D ++ G DG+T+D+EGYLWNA ++VRY P+G +DR++ +P + Sbjct: 179 DLSGERVFCHVDRSEGGAADGATVDSEGYLWNALVYAGKLVRYTPEGEVDRIIEMPVKKV 238 Query: 239 SCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRFAG 292 + V FGG D LYVT+ + + G+LFA+ V G+ E RFAG Sbjct: 239 TSVMFGGENLDVLYVTSMAQPPLPRFPEDNQLRGSLFAIYDLGVTGVAERRFAG 292 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: 304 Number of extensions: 18 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: 292 Length of database: 292 Length adjustment: 26 Effective length of query: 266 Effective length of database: 266 Effective search space: 70756 Effective search space used: 70756 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