Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_012401959.1 BPHY_RS13115 gamma-glutamyl-phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000020045.1:WP_012401959.1 Length = 423 Score = 265 bits (676), Expect = 4e-75 Identities = 147/418 (35%), Positives = 240/418 (57%), Gaps = 12/418 (2%) Query: 292 DSNARDMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGL 351 D D+ AR +SR + S+ + L +A A+E T++ N D+A A++ G Sbjct: 4 DQYMTDLGRRARHASRAMARASTAAKNAALEAVAVAIEREADTLRQANARDLARARDKGH 63 Query: 352 EESMVARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIV 411 + + + RL ++ + ++ +R++A + DPIG + G+ + + PLGV+ I+ Sbjct: 64 DAAFIDRLTLSDKALKTMVEGLRQVAALADPIGEISNLKFRPSGIQVGQMRVPLGVIGII 123 Query: 412 FESRPDALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV-- 468 +ESRP+ + A+L ++SGN +L+GG EA N L ++I + + + + + + +V Sbjct: 124 YESRPNVTIDAAALCLKSGNATILRGGSEALECNTALARLIGEGLDKAGLPQEAVQVVET 183 Query: 469 TSREEIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMA 528 + R + L+ + D +D+++PRG L+ ++ +++P++ H DGICHVYVD D A Sbjct: 184 SDRAAVGKLITMTDYVDVIVPRGGKSLIARLMEESRVPMIKHLDGICHVYVDDRADVAKA 243 Query: 529 KRIVSDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN-- 586 + +AK CN METLLV + + + VL L + V L A +L Sbjct: 244 LNVCDNAKTHRYGTCNTMETLLVARGIAAH-VLPALGKLYREKEVELRVDSAARAVLTEA 302 Query: 587 ----IPEA--RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFL 640 + +A + EY A V+VV+ + AI HI+ +GS HTD IVTEDH+ A FL Sbjct: 303 GVAPLVDATEEDWRTEYLAPVLAVKVVDGIDDAIGHINEYGSHHTDAIVTEDHDRAMRFL 362 Query: 641 RQVDSAAVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698 R+VDSA+V NASTRF+DGF FGLGAE+G+S ++HARGPVG+EGL + ++++ G G+ Sbjct: 363 REVDSASVMVNASTRFADGFEFGLGAEIGISNDKLHARGPVGLEGLTSLKYVVLGHGE 420 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: 621 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: 423 Length adjustment: 36 Effective length of query: 681 Effective length of database: 387 Effective search space: 263547 Effective search space used: 263547 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: 53 (25.0 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