Align 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60) (characterized)
to candidate 8501602 DvMF_2320 6-phosphogluconate dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::Q8ZLV8 (296 letters) >FitnessBrowser__Miya:8501602 Length = 287 Score = 120 bits (301), Expect = 4e-32 Identities = 76/258 (29%), Positives = 127/258 (49%), Gaps = 1/258 (0%) Query: 5 VGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETASTAKAIAEQCDVIIT 64 + +GLG MG+ M+ NLLKAG+ + V +R A ++A GA A+T K A D ++ Sbjct: 4 IAVLGLGAMGRRMAANLLKAGHQVTVWNRTARAAEPLLALGATQAATPKQAAAGADFVLA 63 Query: 65 MLPNSPHVKEVAL-GENGIIEGAKPGTVLIDMSSIAPLASREISDALKAKGVEMLDAPVS 123 M+ + V L E G G +PG + +D S+++ +++ +GV +L+ PVS Sbjct: 64 MVRDDAASATVWLDAETGAFAGMRPGAIAMDSSTLSVDWIKKLGAEAANRGVTLLETPVS 123 Query: 124 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNI 183 G P+A L +VGG + ++ AM +V HTGDIGAG +TKLA ++ + + Sbjct: 124 GSLPQADAAQLIFLVGGSADACRQAEPVLLAMGSAVNHTGDIGAGALTKLATNALLGVQV 183 Query: 184 AAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDLA 243 A++E + + + G + + I G S ++ F ++L KD Sbjct: 184 TAIAELIGMLRRNGADAQKIMGIIAGTAVWSPYAQRAIGALLSGEAPVMFPVELVEKDFG 243 Query: 244 NALDTSHGVGAQLPLTAA 261 AL+ + A + AA Sbjct: 244 YALEAAGSPDAAPTIAAA 261 Lambda K H 0.316 0.132 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: 184 Number of extensions: 7 Number of successful extensions: 2 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: 296 Length of database: 287 Length adjustment: 26 Effective length of query: 270 Effective length of database: 261 Effective search space: 70470 Effective search space used: 70470 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: 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