Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate PfGW456L13_3453 Short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3453 Length = 272 Score = 150 bits (378), Expect = 4e-41 Identities = 100/255 (39%), Positives = 142/255 (55%), Gaps = 19/255 (7%) Query: 56 RLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAE--SDAITTQLLDV 113 RL GK C+IT AG+GIGR SAL AR GA V+ TD+ A + QA+AAE +A+ Q +DV Sbjct: 7 RLDGKVCVITGAGSGIGRASALRFAREGATVVVTDLFAESAQAVAAEIGVNALVLQ-VDV 65 Query: 114 TDAAAITAL----VAAHGPFDVLFNCAGYVHQGSILDCD-----EPAWRRSFSINVDAMY 164 A+ + V G DVLFN A Y + + D D + +NV Sbjct: 66 GQEDALREMVEQTVRTFGRIDVLFNNAVYRNPATTRDIDFINFNTELFHNCMRVNVLGGV 125 Query: 165 YTCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGV 224 CK LP ML +G GSI+ SS SSI G ++F YG +KAA+ + IAA + +G+ Sbjct: 126 LACKYALPHMLAQGSGSILFTSS-TSSIAGEISQFSYGASKAALNWYVQTIAATFGKRGI 184 Query: 225 RCNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDES 284 RCN I PG I+TP++ +A+ +F D Q + +LG+P +IA + +LASD++ Sbjct: 185 RCNGILPGVIRTPAMESWA------NEAMKSAFLDLQNVPQLGEPEDIAAMAAFLASDDA 238 Query: 285 SFTTGQTHIIDGGWS 299 ++ G +DGG S Sbjct: 239 AYVNGTLMRVDGGMS 253 Lambda K H 0.320 0.133 0.395 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: 176 Number of extensions: 9 Number of successful extensions: 5 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: 272 Length adjustment: 26 Effective length of query: 274 Effective length of database: 246 Effective search space: 67404 Effective search space used: 67404 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 (21.8 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