Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_077278551.1 B1C78_RS07550 glutamate 5-kinase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_002000365.1:WP_077278551.1 Length = 375 Score = 138 bits (347), Expect = 6e-37 Identities = 106/338 (31%), Positives = 166/338 (49%), Gaps = 31/338 (9%) Query: 4 LDRSRAFARDVKRIVVKVGTAVVTGKGGRLALGRLGALCEQLAELNSDGFEVILVSSGAV 63 + ++R + +R VVK+G+A++T +G L L L EQ+A L S G EV++VSSGAV Sbjct: 1 MTQTRKQLGEARRWVVKIGSALLTNEGRGLDLAALTGWAEQIARLRSTGREVVVVSSGAV 60 Query: 64 GLGRQRLRYRQLVNSSFADLQKPQTELDGKACAGVGQSSLMAYYETMFDQLDVTAAQLLV 123 G RL + +P + +A A VGQ L+ YE++F + + AAQ+L+ Sbjct: 61 AEGMSRLGW----------TARPHALYELQAAAAVGQMGLVQAYESIFQRHGLRAAQVLL 110 Query: 124 NDSSFRDKDFRKQLNETVKSMLDLRVIPIFNENDAISTRRAPYQDSSGIFWDNDSLAALL 183 D+ T++++ L VIP+ NEND ++T F DND+LAAL+ Sbjct: 111 THEDLSDRRRYLNARSTLRTLTGLGVIPVVNENDTVATDEIR-------FGDNDTLAALV 163 Query: 184 ALELKADLLILLSDVEGLYTGPPSDPNSKLIHTFVKEKHQDEI-----TFGDKSRLGRGG 238 +A +L++L+D +GLY P + + + + D + TFG LGRGG Sbjct: 164 GNLTEARILVILTDQQGLYDRDPRAHANAALISEGRATDPDLLKLAAPTFG---HLGRGG 220 Query: 239 MTAKVKAAVNAAYAGIPVIITSGYSAENIDKVLRGLRVGTLFHQDARLWAPITDSNARDM 298 M K++AA AA +G +I SG ++++ G +GTL D PI AR Sbjct: 221 MATKLQAAARAARSGTYTLIASGREPRVLERIAAGEPLGTLLCPDRE---PIA---ARKQ 274 Query: 299 AVAARESSRKLQALSSEDRKKILLDIADALEANVTTIK 336 +A + S+ L S + + L VT +K Sbjct: 275 WIAGQLVSKGELVLDSGAARVVRESGRSLLPVGVTHVK 312 Lambda K H 0.318 0.135 0.378 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: 493 Number of extensions: 24 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 717 Length of database: 375 Length adjustment: 35 Effective length of query: 682 Effective length of database: 340 Effective search space: 231880 Effective search space used: 231880 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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