Align glycolaldehyde oxidoreductase medium subunit (characterized)
to candidate GFF2053 PGA1_c20860 molybdenum hydroxylase family protein, medium subunit
Query= metacyc::MONOMER-18072 (282 letters) >FitnessBrowser__Phaeo:GFF2053 Length = 262 Score = 118 bits (295), Expect = 2e-31 Identities = 86/273 (31%), Positives = 133/273 (48%), Gaps = 17/273 (6%) Query: 5 DFTYVRVSSSEEATKFLESHDDARPLAGGQSLIPMLKLRVISPNYIVDLNPITSLSYVRS 64 +F + + S+ +A K L +DA+ L GGQ+LIP LK R+ P+ +V L+ I + V Sbjct: 3 EFEFEKPSTIADAVKAL-GEEDAQALGGGQTLIPTLKQRLAMPSTLVSLSGIEEMKGVCP 61 Query: 65 SFNSTKIGALTRYNEILKNDLVRVNVPLLHQAVRVVGDMQVRNLGTIGGSAANADPSADI 124 + IG T + E+ + P L +GD VRN GTIGGS AN DPSA Sbjct: 62 DGDGLAIGGATTHGEV--EAATADSYPALSALAGQIGDPAVRNRGTIGGSLANNDPSACY 119 Query: 125 PTVLTALNAEIILSSASGNRSVNALDFFKGAFATDLRKGEIISEIVLPNLEGYRTIYKKV 184 P A A I+ + R + A D+F+G F T L +GEII+ I LP + Y+K Sbjct: 120 PAAALASGATIV----TNTREIAADDYFQGLFTTALEEGEIITNIRLPVPQSAH--YEKF 173 Query: 185 VRRAGDFALVSLALAIKLRQNEIEDIRLAYGGVGERPFRALEVEKSVMGKRLNDELVEEI 244 V+ A FALV + +A E +R+A G E ++ + + + ++ + Sbjct: 174 VQPASRFALVGVFVA-----RFAEGVRVAVTGASEEGVFRWSAAEAALSANFSPDAIDGL 228 Query: 245 VSKVSSQVNPPSDTRGSSWYRREVMKVITRKAL 277 + D G+ YR ++ VIT++A+ Sbjct: 229 TVDPDGMI---GDLHGTKAYRAHLVGVITKRAV 258 Lambda K H 0.317 0.134 0.367 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: 149 Number of extensions: 9 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: 282 Length of database: 262 Length adjustment: 25 Effective length of query: 257 Effective length of database: 237 Effective search space: 60909 Effective search space used: 60909 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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