Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate CCNA_01882 CCNA_01882 SMP-30/gluconolaconase/LRE-like protein
Query= uniprot:B2UIY8 (300 letters) >FitnessBrowser__Caulo:CCNA_01882 Length = 293 Score = 169 bits (429), Expect = 5e-47 Identities = 101/265 (38%), Positives = 136/265 (51%), Gaps = 12/265 (4%) Query: 9 VERIGNMQCGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPLPEMAGCIAMAP 68 VE IG +C +GESP+W A LYW D +WR++ F+ + + P P+ G + + Sbjct: 5 VEIIGKERCRLGESPLWDADAGVLYWVDSMAPAIWRYDPFTSEQRSIPAPKPIGSVVLGR 64 Query: 69 NGWAMA-METGIFLAPPPSPGIELGPLQRLATVAHARPDMRFNDGRCDRQGRFWAGTMVL 127 G +A + G++ ++ G +A P RFNDG+ DRQGRF GTM + Sbjct: 65 PGELIAGLADGVYRVQ-----LDTGAFTPIALPDTLAPIERFNDGKADRQGRFVTGTMAM 119 Query: 128 DTSLGLPLGKLYRLDAAAARTGRVDAVIDDLIVPNGLAFSPEGKTMYLSDSHASRQTVWA 187 G +GKLYR A A I+ + N FSP G T+Y +DS R VWA Sbjct: 120 HNETGR-IGKLYRFSAGGAWEVLPTEPIE---IANSTCFSPSGDTLYFADS--LRHMVWA 173 Query: 188 FDYDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDAGFVHRFTPDGRLDRSI 247 F YD TG +R F D + PDGA VDA+G W+ A + R +PDGRLDR + Sbjct: 174 FSYDPKTGAVGEKRDFFDTTGFNSAPDGATVDAEGHIWLALVQAQKLIRISPDGRLDRVV 233 Query: 248 AIPTSKPAMCAFGGPGLDTLFVTSI 272 P + AFGG LD L+VTSI Sbjct: 234 ESPAPFCSCPAFGGEDLDILYVTSI 258 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: 380 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: 293 Length adjustment: 26 Effective length of query: 274 Effective length of database: 267 Effective search space: 73158 Effective search space used: 73158 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