Align L-arabinonolactonase (characterized, see rationale)
to candidate WP_057509054.1 ABB28_RS13170 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:A0A1I2AUG6 (300 letters) >NCBI__GCF_001431535.1:WP_057509054.1 Length = 308 Score = 219 bits (559), Expect = 5e-62 Identities = 131/292 (44%), Positives = 164/292 (56%), Gaps = 16/292 (5%) Query: 12 TLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLALCEADGWLLLGL 71 TLGE I WC RE+ L+WTDI +WR P G + W P R+G LALCE+ G LLLG+ Sbjct: 22 TLGESITWCARERVLWWTDINGRRIWRGNPDTGNAQWWSTPGRVGSLALCES-GRLLLGM 80 Query: 72 ATRLAFFRPEDDLLLPLVSVEP--DLPT-----RLNDGACDRQGRFVFGTLHEPAAGETR 124 L F P + ++ E ++P R+NDG DR G FVFG ++E A R Sbjct: 81 EKALYFADPSREEPGAGLNCEQVCEVPMDGAALRINDGRLDRAGNFVFGCINEDPA---R 137 Query: 125 QPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGDRCG-- 182 F++ + L L L + I+N + F PDG+ MY+CDS I Y Sbjct: 138 ARAARFHQYSIAQGLRALALEPVAIANGICFDPDGQGMYYCDSLQGRIMHAGYDAATATV 197 Query: 183 -EPRVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPATQPTRP 241 +PRVFA +D EPDG+ VDA G +W AQWG GRVVRY+ G VDRI+ VPA QPT Sbjct: 198 SDPRVFAVIDGG-AEPDGAVVDADGRVWGAQWGAGRVVRYSAAGEVDRILPVPALQPTCV 256 Query: 242 AFGDSPLDTLYITSARDGLSSAALATQPLAGALFAAD-AGASGLPEPRFRGA 292 AF L TLY+TSARDGL A L QP +G +F GA GLP+ RF A Sbjct: 257 AFAGDGLGTLYVTSARDGLDVAMLQDQPTSGGVFRVSLEGARGLPDLRFTDA 308 Lambda K H 0.321 0.139 0.451 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: 411 Number of extensions: 28 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: 300 Length of database: 308 Length adjustment: 27 Effective length of query: 273 Effective length of database: 281 Effective search space: 76713 Effective search space used: 76713 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 (21.8 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