Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate PfGW456L13_3458 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= uniprot:A0A4R8NY47 (263 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3458 Length = 251 Score = 105 bits (261), Expect = 1e-27 Identities = 76/254 (29%), Positives = 125/254 (49%), Gaps = 17/254 (6%) Query: 17 LAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFPCN 76 LAGKR+++TGG GIGAA+V+AFV +GA V LD+ S D C+ Sbjct: 3 LAGKRIIVTGGARGIGAAVVKAFVEEGAHVVSLDLGEAAS-----ITGDGGGWAHSRVCD 57 Query: 77 LMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFFCAQ 136 + + +++ A F + G+D+L++ A ++ +T W++ AVN R F + Sbjct: 58 IADSQSVDAAFAWASEQLNGLDVLVHAAGIAPNASADSITLDEWEKVFAVNTRGTFLTNR 117 Query: 137 AVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVNAI 196 A + + GG I+NF S + LG P Y +K + T +AR++G G+ VNAI Sbjct: 118 AAYE-LLKGSGGRIINFASAAGVLGQPGKAHYAASKGAVLAWTRTVAREWGPLGITVNAI 176 Query: 197 IPGAIRTP-----RQTLLWHTPEEEAKILAAQCLPV----RVDPHDVAALALFLSSDSGA 247 P A+ TP R ++ ++ +A Q +P+ D+A + +FL+ D Sbjct: 177 AP-AMWTPMYDATRASMSAEQLQQHDAYMAGQ-VPIGGKLGEPARDLAPVLVFLAGDGSR 234 Query: 248 KCTGREYYVDAGWL 261 TG+ +D G + Sbjct: 235 FVTGQTLVIDGGMM 248 Lambda K H 0.322 0.137 0.417 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: 163 Number of extensions: 8 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: 263 Length of database: 251 Length adjustment: 24 Effective length of query: 239 Effective length of database: 227 Effective search space: 54253 Effective search space used: 54253 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: 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