Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate PfGW456L13_2118 L-arabinolactonase (EC 3.1.1.15)
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2118 Length = 291 Score = 142 bits (359), Expect = 7e-39 Identities = 102/290 (35%), Positives = 138/290 (47%), Gaps = 35/290 (12%) Query: 19 VGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAPNGWAM-AMET 77 +GE P W A QALYW DI G+ R W +PE +G A+ A+ + Sbjct: 13 LGEGPFWDAPTQALYWVDIAGKQALR--LIGANVQIWQMPEHVSAFIPCESGDALVALSS 70 Query: 78 GIFLAPPPSPGIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVLDTSLG---LP 134 G++ SPG L P L VA +P R N+ RCD QGR W GTM + LP Sbjct: 71 GVYRLDLDSPG--LAPRLTLFCVADPQPGNRPNEARCDAQGRLWLGTMQNNIGANGEDLP 128 Query: 135 L----GKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDS-------HASRQ 183 + G L+R+D R GRV ++ +L +PN L +S + ++Y DS H R Sbjct: 129 IVHRSGGLFRID----RAGRVAPLLRNLGIPNTLLWSDDATSVYFGDSLDGTLYRHFIR- 183 Query: 184 TVWAFDYDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRL 243 T A D PH R G PDG+A+DA+G W D + R + DG++ Sbjct: 184 TDGALDAPQVWFGPHER----------GVPDGSAMDAEGFIWNARWDGNCLLRLSLDGKV 233 Query: 244 DRSIAIPTSKPAMCAFGGPGLDTLFVTSIRIG-DDPLSGATFAVRPGVTG 292 DR I +P S+P C FGG L TL++TS PL GA ++ V G Sbjct: 234 DRIIELPVSRPTSCVFGGSDLKTLYITSAASPLGHPLDGAVLSIAVDVPG 283 Lambda K H 0.322 0.140 0.466 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: 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: 291 Length adjustment: 26 Effective length of query: 274 Effective length of database: 265 Effective search space: 72610 Effective search space used: 72610 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