Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate GFF443 PGA1_c04540 putative d-galactonate dehydratase
Query= BRENDA::A9CEQ8 (378 letters) >FitnessBrowser__Phaeo:GFF443 Length = 410 Score = 146 bits (368), Expect = 1e-39 Identities = 109/363 (30%), Positives = 168/363 (46%), Gaps = 34/363 (9%) Query: 29 RAHVLVEIECDDGTVGWGEC----LGPARPNAAVVQAYSGWLIGQDPRQTEKIWAVLYNA 84 R +LV++ D G GWGEC +GP + + + G +P E ++ Y++ Sbjct: 21 RYWILVKVTTDTGITGWGECYAASVGPDAMTHVIRDVFERHMQGMNPENIEWMFRRAYSS 80 Query: 85 LRDQGQRGLSLTALSGIDIALWDIKGKHYGASISMLLGGRWRESVRAYA-TGSFKRDNVD 143 Q + A SG++IA WDI GK + L+GGR + +RAY ++D Sbjct: 81 GFTQRPDLSVMGAFSGLEIACWDILGKDRDRPVHALIGGRMNDRLRAYTYLYPLPHHDID 140 Query: 144 RVSDNASEMAERRA-----EGFHACK-------------IKIGFGVEEDLRVIAAVREAI 185 N E+A A +G+ A K + + + + A+REA+ Sbjct: 141 AFW-NTPELAAESAIAAVEKGYTAVKFDPAGPYTMRGGHMPAQSDITQSVAFCRAIREAV 199 Query: 186 GPDMRLMIDANHGYTVTEAITLGDRAAGFGIDWFEEPVVPEQLDAYARVRAGQPIPVAGG 245 G L+ + +T AI LG + WFEEP P+ + ARV IPVA G Sbjct: 200 GDRADLLFGTHGQFTPAGAIRLGQALESYEPLWFEEPTPPDLVADMARVADRVRIPVATG 259 Query: 246 ETWHGRYGMWQALSAGAVDILQPDLCGCGGFSEIQKIATLATLHGVRIVPHVWGTGVQIA 305 E + L AGA +ILQP L GG E +KIA +A + G ++ PH++ V+ A Sbjct: 260 ERLTTKAEFAAILRAGAAEILQPALGRSGGIWETKKIAAIAEVFGAQMAPHLYAGPVEWA 319 Query: 306 AALQFMAAMTPDPVRVNPIEPIMEFDRTHNPFRQAVLREPLEAVNGVVTIPDGPGLGIEI 365 A +Q +AA P+ + + IE PF A++++ + +G V D PGLGIE+ Sbjct: 320 ANIQ-LAASIPNLLMIETIE---------TPFHTALIKQGITVEDGFVIPSDTPGLGIEV 369 Query: 366 NRD 368 + D Sbjct: 370 DED 372 Lambda K H 0.321 0.138 0.431 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: 487 Number of extensions: 31 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: 378 Length of database: 410 Length adjustment: 31 Effective length of query: 347 Effective length of database: 379 Effective search space: 131513 Effective search space used: 131513 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: 50 (23.9 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