Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate GFF719 PGA1_c07340 Gluconolactonase
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__Phaeo:GFF719 Length = 290 Score = 118 bits (295), Expect = 2e-31 Identities = 90/287 (31%), Positives = 136/287 (47%), Gaps = 27/287 (9%) Query: 16 QCGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAPNGWAMAM 75 +C +GE P+WH + L+W DI + L + G+ W + C++ A GW Sbjct: 19 RCTLGEGPLWHPTRRQLFWFDILEKRLL--SVAGGKEIIWQFDD---CVSAA--GWVD-- 69 Query: 76 ETGIFLAPPPSP---GIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVLDTSLG 132 ET + +A + IE G L + +P R NDGR D G FW GTM + G Sbjct: 70 ETTLIMASARALWRFDIESGARTHLIDLEADQPLTRSNDGRADPWGGFWIGTMGYNAEFG 129 Query: 133 LPLGKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHAS---RQTVWAFD 189 L G +YR G + ++ + + N + F+P+ Y +D+ RQ + A D Sbjct: 130 L--GAIYRY-----YQGELRQLVANQTITNAICFAPDKSCAYFTDTKTGKIMRQPLAAED 182 Query: 190 YDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRLDRSIAI 249 G P VFID++ PDGA VDA+G +W A V +TP G L ++ Sbjct: 183 -GWPIGAPS---VFIDLSGEDFGPDGAIVDAEGRFWNAQWGASRVAVYTPTGELTEIYSV 238 Query: 250 PTSKPAMCAFGGPGLDTLFVTSIRIG-DDPLSGATFAVRPGVTGLPE 295 PT++ + A GG L LF+T+ G DDP +G T++++ G E Sbjct: 239 PTAQASCPALGGASLSYLFITTAADGLDDPAAGKTYSIQTTAKGQRE 285 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: 292 Number of extensions: 16 Number of successful extensions: 3 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: 290 Length adjustment: 26 Effective length of query: 274 Effective length of database: 264 Effective search space: 72336 Effective search space used: 72336 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