Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate Pf6N2E2_5966 L-arabinolactonase (EC 3.1.1.15)
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5966 Length = 291 Score = 131 bits (330), Expect = 2e-35 Identities = 94/296 (31%), Positives = 138/296 (46%), Gaps = 45/296 (15%) Query: 19 VGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAPNGWAMA-MET 77 +GE P W QALYW DI G+ R W +PE +G A+ + + Sbjct: 13 LGEGPFWDEPTQALYWVDIAGKQALR--LIGANVQIWQMPEHVSAFIPTQSGDALVTLSS 70 Query: 78 GIFLAPPPSPGIELGPLQRLATVAHARPDM--RFNDGRCDRQGRFWAGTM---VLDTSLG 132 G++ SPG+E RL + A P + R N+ RCD G+ W GTM + + + Sbjct: 71 GVYRLDLDSPGLE----PRLTLLCMADPQLGNRANEARCDALGQLWLGTMQNNIGENAED 126 Query: 133 LPL----GKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHASRQTVWAF 188 LP+ G L+R+ GRV ++ L +PN L +SP+G T+Y +S Sbjct: 127 LPIERRSGGLFRVSG----DGRVMPLLRGLGIPNTLLWSPDGTTVYFGES---------- 172 Query: 189 DYDIDTGTPHNRRVFIDMNAYP----------GRPDGAAVDADGCYWICGNDAGFVHRFT 238 +D GT + + D + P G PDG+A+DA G W D + R Sbjct: 173 ---LD-GTLYRHFIHPDGSLAPAEVWFGPHPRGGPDGSAMDARGYIWNARWDGSCLLRLN 228 Query: 239 PDGRLDRSIAIPTSKPAMCAFGGPGLDTLFVTSIRIG-DDPLSGATFAVRPGVTGL 293 P G++DR I +P S+P C FGG L TL++TS PL GA ++R + G+ Sbjct: 229 PQGQVDRVIELPVSRPTSCVFGGDDLKTLYITSAASPLGHPLDGAVLSMRVDIPGV 284 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: 377 Number of extensions: 25 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