Align glycerol dehydrogenase (EC 1.1.1.6) (characterized)
to candidate 14736 b0599 predicted oxidoreductase (NCBI)
Query= BRENDA::Q9WYQ4 (364 letters) >FitnessBrowser__Keio:14736 Length = 362 Score = 166 bits (421), Expect = 7e-46 Identities = 120/369 (32%), Positives = 184/369 (49%), Gaps = 28/369 (7%) Query: 2 ITTTIFPGRYVQGAGAINIL-----EEELSR----FGERAFVVIDDFVDKNVLGENFFSS 52 I + P Y G+ N L +E+LSR +G+RA + + Sbjct: 6 IRVVVGPANYFSHPGSFNHLHDFFTDEQLSRAVWIYGKRAIAAAQTKLPP---------A 56 Query: 53 FTKVRVNKQIFGGECSDEEIERLSGLVEEETDVVVGIGGGKTLDTAKAVAYKLKKPVVIV 112 F +F G CS+ ++++L+ ++ VV+G+GGG LDTAKA+A +L P V V Sbjct: 57 FGLPGAKHILFRGHCSESDVQQLAAESGDDRSVVIGVGGGALLDTAKALARRLGLPFVAV 116 Query: 113 PTIASTDAPCSALSVIYTPNGEFKRYLFLPRNPDVVLVDTEIVAKAPARFLVAGMGDALA 172 PTIA+T A + LSV Y G+ Y +VLV+ EI+ AP ++L+AG+GD LA Sbjct: 117 PTIAATCAAWTPLSVWYNDAGQALHYEIFDDANFMVLVEPEIILNAPQQYLLAGIGDTLA 176 Query: 173 TWFEA-ESCKQKYAPNMTGRLGSMTAYALARLCYETLLEYGVLAKRSVEEKSVTPA---- 227 W+EA Q +T RLG A A+ + LL A + + +T + Sbjct: 177 KWYEAVVLAPQPETLPLTVRLGINNAQAIR----DVLLNSSEQALSDQQNQQLTQSFCDV 232 Query: 228 LEKIVEANTLLSGLGFESGGLAAAHAIHNGLTVLENTHKYLHGEKVAIGVLASLFLTDKP 287 ++ I+ ++ GLG +AAAHA+HNGLTVL T K+LHG KVA G+L L + Sbjct: 233 VDAIIAGGGMVGGLGDRFTRVAAAHAVHNGLTVLPQTEKFLHGTKVAYGILVQSALLGQD 292 Query: 288 RKMIEEVYSFCEEVGLPTTLAEIGLDGVSDEDLMKVAEKACDKNETIHNEPQPVTSKDVF 347 ++ ++ + LPTTLAE+ +D + ++ KV E+IH P +T + Sbjct: 293 -DVLAQLTGAYQRFHLPTTLAELEVDINNQAEIDKVIAHTLRPVESIHYLPVTLTPDTLR 351 Query: 348 FALKAADRY 356 A K + + Sbjct: 352 AAFKKVESF 360 Lambda K H 0.318 0.135 0.384 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: 333 Number of extensions: 14 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: 364 Length of database: 362 Length adjustment: 29 Effective length of query: 335 Effective length of database: 333 Effective search space: 111555 Effective search space used: 111555 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 (21.7 bits) S2: 49 (23.5 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