Align L-arabinolactonase (EC 3.1.1.15) (characterized)
to candidate WP_057509054.1 ABB28_RS13170 SMP-30/gluconolactonase/LRE family protein
Query= reanno::HerbieS:HSERO_RS05225 (292 letters) >NCBI__GCF_001431535.1:WP_057509054.1 Length = 308 Score = 242 bits (618), Expect = 7e-69 Identities = 121/292 (41%), Positives = 170/292 (58%), Gaps = 7/292 (2%) Query: 5 LLVDGHHELGEGVLWCDRSQSVFWTDIHASRLWNHDPQTGLTRSWGMPERLCCYAFTADP 64 L D LGE + WC R + ++WTDI+ R+W +P TG + W P R+ A + Sbjct: 15 LAFDSRCTLGESITWCARERVLWWTDINGRRIWRGNPDTGNAQWWSTPGRVGSLAL-CES 73 Query: 65 QQLLIGLESRLAFFNLSTG------TIAPICRIEDDLPSTRLNDGRCDRQGRFVFGTLNE 118 +LL+G+E L F + S +C + D + R+NDGR DR G FVFG +NE Sbjct: 74 GRLLLGMEKALYFADPSREEPGAGLNCEQVCEVPMDGAALRINDGRLDRAGNFVFGCINE 133 Query: 119 DAGRAPIASFYRLNTDLTLERLSLPSIAISNSICFSLDGKLMYHCDSMAGKIMVCDYDTA 178 D RA A F++ + L L+L +AI+N ICF DG+ MY+CDS+ G+IM YD A Sbjct: 134 DPARARAARFHQYSIAQGLRALALEPVAIANGICFDPDGQGMYYCDSLQGRIMHAGYDAA 193 Query: 179 SGAVGGQRVFADVAQPGGPDGSTIDAEGYLWNAQWGGARVVRYAPDGRIDRVVAIPTSQP 238 + V RVFA + PDG+ +DA+G +W AQWG RVVRY+ G +DR++ +P QP Sbjct: 194 TATVSDPRVFAVIDGGAEPDGAVVDADGRVWGAQWGAGRVVRYSAAGEVDRILPVPALQP 253 Query: 239 SCVAFGGAQFDTLYVTTAHEGMSAEQRAADPQAGALFAVALADVRGLPEVRF 290 +CVAF G TLYVT+A +G+ P +G +F V+L RGLP++RF Sbjct: 254 TCVAFAGDGLGTLYVTSARDGLDVAMLQDQPTSGGVFRVSLEGARGLPDLRF 305 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: 372 Number of extensions: 22 Number of successful extensions: 2 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: 308 Length adjustment: 27 Effective length of query: 265 Effective length of database: 281 Effective search space: 74465 Effective search space used: 74465 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