Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate SMc03777 SMc03777 gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Smeli:SMc03777 Length = 427 Score = 272 bits (695), Expect = 3e-77 Identities = 143/423 (33%), Positives = 246/423 (58%), Gaps = 22/423 (5%) Query: 292 DSNARDMAVA--ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEA 349 D NA + + A+ ++R L S+E + L+ +A + I A N LD+ +A+E+ Sbjct: 10 DVNAMMLEIGRRAKAAARPLATASAERKHAALVAMAGVIVTRTAEILAANALDLENARES 69 Query: 350 GLEESMVARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLL 409 G+ + + RL +T +I +A +R +A++ DP+G V+ + + +GL +E+ +PLGV+ Sbjct: 70 GVASAFIDRLTLTESRIRDMADGIRAIAELIDPVGEVISEWDRPNGLHIERVRTPLGVIG 129 Query: 410 IVFESRPDALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPETVGGKLIGL-- 467 +++ESRP+ +L +++GN ++L+GG ++ S+ +H +T+ + K+ GL Sbjct: 130 VIYESRPNVTADAGALCLKAGNAVILRGGSDSFHSSRAIHACLTEGL------KVAGLPE 183 Query: 468 -------VTSREEIPDLLK-LDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYV 519 V R + +L L+ ID+++PRG LV +++N ++PV H +G+CH+YV Sbjct: 184 DAIQMVPVADRAAVGAMLTGLNGAIDVIVPRGGKSLVARVQNEARVPVFAHLEGLCHIYV 243 Query: 520 DKACDTDMAKRIVSDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGP 579 D + D DMAK+IV +AK+ C A ETLL+ ++ + L+ AL G + Sbjct: 244 DASADRDMAKKIVVNAKMRRTGICGAAETLLIDRNAAEKFA-KPLLEALVDAGCEVRASD 302 Query: 580 RASKI---LNIPEARSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVA 636 + + L + EY + +V+ + GAI+HI+ SAHT+ ++ ED V Sbjct: 303 DLASVMPGLKAATDEDWATEYLDAIISARLVDGISGAIEHINTWSSAHTEAVIAEDPAVV 362 Query: 637 ELFLRQVDSAAVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGK 696 E F ++DSA + HNAST+F+DG FG+G E+G++TG++HARGPVGVE L + ++ +RG Sbjct: 363 ERFFSEIDSAILLHNASTQFADGGEFGMGGEIGIATGKMHARGPVGVEQLTSFKYRVRGT 422 Query: 697 GQV 699 GQV Sbjct: 423 GQV 425 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: 616 Number of extensions: 32 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: 427 Length adjustment: 36 Effective length of query: 681 Effective length of database: 391 Effective search space: 266271 Effective search space used: 266271 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 09 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