Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate Ac3H11_2081 Gluconolactonase (EC 3.1.1.17)
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2081 Length = 316 Score = 184 bits (468), Expect = 2e-51 Identities = 112/295 (37%), Positives = 158/295 (53%), Gaps = 23/295 (7%) Query: 19 VGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAPNGW-AMAMET 77 +GESP WH E++LYW DI G+ + W+ SG+ W +P GC A A +G + + Sbjct: 13 LGESPFWHPTEKSLYWCDIQGQAVHAWHPESGRHRQWRMPSEPGCCAPAADGQLVIGLRN 72 Query: 78 GIFLAPPPSPGIELGPLQRLATVAHARPD---MRFNDGRCDRQGRFWAGTMVLDTSLGLP 134 G +L + L LA + + D +R NDGRCD GRFWAG+++ T P Sbjct: 73 GFYLLDTAKGSTDPTALTCLALLPPEQHDTAVLRLNDGRCDTAGRFWAGSVI--TPRTAP 130 Query: 135 LGKLYRL--DAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHASRQTVWAFDYDI 192 L+ L DAA+A RV + D NGLAFSP+ +T+Y S++ R + FD+D+ Sbjct: 131 NAALWCLQADAASATGYRVRHMAGDNFTANGLAFSPDDRTLYWSNTPEHR--IDQFDFDV 188 Query: 193 DTGTPHNRRVFIDMNA------YPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRLDRS 246 DTG NRR ++ + Y GRPDGAAVD +G YW+ + V + +P G + + Sbjct: 189 DTGAISNRRPWVQFDRKVEGQPYGGRPDGAAVDVEGNYWVAMYEGACVLQLSPAGEVLQR 248 Query: 247 IAIPTSKPAMCAFGGPGLDTLFVTSIRIG-------DDPLSGATFAVRPGVTGLP 294 I +P P M FGG L TLF+TS R G + +G+ F+VR V GLP Sbjct: 249 IEVPVQCPTMVCFGGEDLRTLFITSARAGRPVEEREAEVPAGSLFSVRVTVAGLP 303 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: 394 Number of extensions: 31 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: 300 Length of database: 316 Length adjustment: 27 Effective length of query: 273 Effective length of database: 289 Effective search space: 78897 Effective search space used: 78897 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