Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate GFF1427 PS417_07255 calcium-binding protein
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >FitnessBrowser__WCS417:GFF1427 Length = 292 Score = 193 bits (490), Expect = 4e-54 Identities = 108/293 (36%), Positives = 160/293 (54%), Gaps = 4/293 (1%) Query: 1 MNVQLLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAF 60 M +++LVD LGEG +W Q ++W D R+ R+W + +++ A Sbjct: 1 MRIEVLVDVKTTLGEGPVWDVEQQRLYWIDSADGRILRCTDDGRELRAWEVGQKIGSMAL 60 Query: 61 TADPQQLLIGLESRLAFFNLSTGTIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNEDA 120 D + ++ L++ + +L +G + I E LP RLNDG+ DRQGRF+FG+++ Sbjct: 61 RQDGESAIVALQNGVHTLDLKSGELNLIADPEPHLPDNRLNDGKVDRQGRFIFGSMDTQE 120 Query: 121 GRAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTASG 180 A A YRL+ DL+L L I +SN C+S G Y CD+ +G+I DYD A+G Sbjct: 121 DNAS-AKLYRLDADLSLHTLD-EGIIVSNGPCWSPSGDTFYFCDTWSGEIWAYDYDLATG 178 Query: 181 AVGGQRVFADVAQPGG--PDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQP 238 V +R FA V GG DG T+DAEG LW A ++VRY P+G +DR++ +P + Sbjct: 179 NVSNRRTFAKVDTRGGGAADGCTVDAEGCLWQALVYAGKLVRYTPEGVVDRIIQMPVKKV 238 Query: 239 SCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRFA 291 + + FGG DTL+VT+ + A Q GALFA+ V+G+ E RFA Sbjct: 239 TSLTFGGPNLDTLFVTSMAKPPLPRFPADGQQRGALFAITGLGVQGIAERRFA 291 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: 22 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: 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