Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate N515DRAFT_1229 N515DRAFT_1229 L-arabinonolactonase (EC 3.1.1.15)
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__Dyella79:N515DRAFT_1229 Length = 300 Score = 176 bits (445), Expect = 8e-49 Identities = 110/274 (40%), Positives = 145/274 (52%), Gaps = 9/274 (3%) Query: 20 EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVG-FCLPAANGKFVAGLQTG 78 EG +W +R+ AL++ DI++ + R PA G RSW+ P ++G L A+G + GL T Sbjct: 15 EGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLALCEADGWLLLGLATR 74 Query: 79 LAIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDD---GES-EATGRIYRL 134 LA F P D PL EP LP RLNDG D GR FGT+ + GE+ + G YRL Sbjct: 75 LAFFRPEDDLLLPLVSVEPDLP-TRLNDGACDRQGRFVFGTLHEPAAGETRQPIGAFYRL 133 Query: 135 GGDGRCVA-ETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILGDSRVFATIP 193 D + ISN A SPDGRT+Y D+ VI GD G+ RVFA + Sbjct: 134 NADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRVIQCCDYGDR--CGEPRVFARVD 191 Query: 194 NSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDLRTV 253 + G PDG AVDA+GC+W + V RY+P G + +V P T+ AFG L T+ Sbjct: 192 DERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRIVEVPATQPTRPAFGDSPLDTL 251 Query: 254 YATTASKHLDADGRAEEPHAGDLFAFRVSVPGMP 287 Y T+A L + A +P AG LFA G+P Sbjct: 252 YITSARDGLSSAALATQPLAGALFAADAGASGLP 285 Lambda K H 0.319 0.139 0.439 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: 389 Number of extensions: 39 Number of successful extensions: 5 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: 295 Length of database: 300 Length adjustment: 26 Effective length of query: 269 Effective length of database: 274 Effective search space: 73706 Effective search space used: 73706 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 (21.7 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