Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_029933890.1 N746_RS0103040 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000711195.1:WP_029933890.1 Length = 417 Score = 271 bits (692), Expect = 6e-77 Identities = 150/409 (36%), Positives = 241/409 (58%), Gaps = 6/409 (1%) Query: 296 RDMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESM 355 +++ AAR +SR L +++ + + LL +A LEA +K+EN D+ + + GL+ +M Sbjct: 8 QNLGQAARAASRVLVTATTQQKDQALLAMAAQLEAQADLLKSENAKDLEAGKANGLDAAM 67 Query: 356 VARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESR 415 + RL + I+ +A +R++A + DPIG V G+ + K PLGV+ I++ESR Sbjct: 68 LDRLAINDKAIAQMAEGLRQIAGLVDPIGEVTDLRYRPSGIQVGKMRVPLGVVGIIYESR 127 Query: 416 PDALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPETVGGKLIGLV---TSRE 472 P+ + A+L ++SGN +L+GG EA SN L I + + K V T RE Sbjct: 128 PNVTIDAAALCLKSGNAAILRGGSEAAFSNRALAACIQAGLEQAGLPKASVQVVETTDRE 187 Query: 473 EIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIV 532 + +L+ + +D++IPRG L+ +I ++PV+ H DGICHVY+D + + A ++ Sbjct: 188 AVGELIAMPKYVDVIIPRGGKGLIARISEHARVPVIKHLDGICHVYIDDDANKEKAIKVA 247 Query: 533 SDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEARS 592 ++K CNAMETLLV + + + +L EL V L G +I+ A + Sbjct: 248 FNSKTHRYGVCNAMETLLVAESVAAD-ILPELAKLYAEKSVELRGCEVTRQIIEAKAATN 306 Query: 593 --FNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650 + EY A +++VV D+ A+ HI ++ S HT+ IVTE++ A F+ Q+DS++V Sbjct: 307 EDWETEYLAPILSIKVVADMQEAMAHITQYSSGHTESIVTENYTKARQFMAQIDSSSVMV 366 Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 NASTRF+DGF +GLGAE+G+ST + HARGPVG+EGL + ++I+ G G + Sbjct: 367 NASTRFADGFEYGLGAEIGISTDKFHARGPVGLEGLTSQKYIVLGDGHI 415 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: 589 Number of extensions: 24 Number of successful extensions: 3 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: 717 Length of database: 417 Length adjustment: 35 Effective length of query: 682 Effective length of database: 382 Effective search space: 260524 Effective search space used: 260524 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