Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate Pf1N1B4_5639 D-serine deaminase (EC 4.3.1.18)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2867 (405 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5639 Length = 405 Score = 761 bits (1966), Expect = 0.0 Identities = 380/405 (93%), Positives = 389/405 (96%) Query: 1 MSSAPNTAAVEKGTAPKGASLVRDVSLPALVLHREALEHNIRWMQAFVSDSGAELAPHGK 60 M SA NTAAVEKG A GA+LVRDVSLPALVLHR+ALEHNIRWMQ FVS+SGAELAPHGK Sbjct: 1 MYSAKNTAAVEKGFAHTGANLVRDVSLPALVLHRDALEHNIRWMQDFVSNSGAELAPHGK 60 Query: 61 TSMTPALFRRQLDAGAWGITLASATQTRAAYAHGVRRVLMANQLVGTPNMALIADLLADP 120 TSMTPALFRRQLDAGAWGITLASATQTRAAYAHGV RVLMANQLVGTPNMALIADLLADP Sbjct: 61 TSMTPALFRRQLDAGAWGITLASATQTRAAYAHGVHRVLMANQLVGTPNMALIADLLADP 120 Query: 121 TFDFYCMVDHPDNVADLGAYFASRGVRLNVMIEYGVVGGRCGCRSEQQVLDLAKAIAAQP 180 TFDFYCMVDHPDNVADLGAYFASRGVRLNVMIEYGVVGGRCGCR+E +VL LAKAIAAQP Sbjct: 121 TFDFYCMVDHPDNVADLGAYFASRGVRLNVMIEYGVVGGRCGCRTETEVLALAKAIAAQP 180 Query: 181 ALALTGIEGYEGVIHGDHAVTGIRDFAASLVRLAVQLQDSGAFAIPKPIITASGSAWYDL 240 ALALTGIEGYEGVIHGDHAV+GIR FA SLVRLAVQLQDSGAFAI KPIITASGSAWYDL Sbjct: 181 ALALTGIEGYEGVIHGDHAVSGIRAFADSLVRLAVQLQDSGAFAIAKPIITASGSAWYDL 240 Query: 241 IAESFEAQNAAGRFLSVLRPGSYVAHDHGIYKEAQCCVLDRRSDLHEGLRPALEVWAHVQ 300 IAESFEAQNA GRFLSVLRPGSYVAHDHGIYKEAQCCVLDRRSDLHEGLRPALEVWAHVQ Sbjct: 241 IAESFEAQNACGRFLSVLRPGSYVAHDHGIYKEAQCCVLDRRSDLHEGLRPALEVWAHVQ 300 Query: 301 SLPEPGFAVIALGKRDVAYDAGLPVPLLRYKAGVVPAEGDDVSVCKVTAVMDQHAFMTVA 360 SLPEPGFAVIALGKRDVAYDAGLPVPLLRYKAGVVPA G+DV CKVTAVMDQHAFMTVA Sbjct: 301 SLPEPGFAVIALGKRDVAYDAGLPVPLLRYKAGVVPAIGEDVGACKVTAVMDQHAFMTVA 360 Query: 361 PGVDLRVGDIISFGTSHPCLTFDKWRVGCLVDEQLNVIETMETCF 405 PGV+LRVGDIISFGTSHPCLTFDKWR+GCLVDEQLNVIETMETCF Sbjct: 361 PGVELRVGDIISFGTSHPCLTFDKWRIGCLVDEQLNVIETMETCF 405 Lambda K H 0.322 0.136 0.413 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: 726 Number of extensions: 18 Number of successful extensions: 1 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: 405 Length of database: 405 Length adjustment: 31 Effective length of query: 374 Effective length of database: 374 Effective search space: 139876 Effective search space used: 139876 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: 50 (23.9 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