Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate 8499847 DvMF_0612 gamma-glutamyl phosphate reductase (RefSeq)
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Miya:8499847 Length = 436 Score = 270 bits (690), Expect = 1e-76 Identities = 156/409 (38%), Positives = 237/409 (57%), Gaps = 8/409 (1%) Query: 298 MAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVA 357 M A+ ++RKL A S + L+ +A LE+ I A N D+A+A+ AG++ + Sbjct: 27 MGKRAKAAARKLAAASPAAKIDALVRLAGLLESREADILAANARDLAAAEAAGMDTPRMD 86 Query: 358 RLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPD 417 RL +TP ++ +AA+ R +A + DP+G V + + +GL++ + PLGV+ I++ESRP+ Sbjct: 87 RLRLTPRIMAEMAAACRHVAGLPDPVGAVETQWQRPNGLLVGRMRIPLGVIAIIYESRPN 146 Query: 418 ALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEI 474 + A L +++GN ++L+GG EA SN L +I +A+ + + + +V T R + Sbjct: 147 VTIDSAILCLKAGNAVILRGGSEAIHSNLALAGLIAEAMSASGLPDDAVQVVSRTDRAAV 206 Query: 475 PDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSD 534 L L+ ID++IPRG L+ + +PVL H G+CH YVD D D A IV + Sbjct: 207 GALCALEQYIDVIIPRGGETLIRAVVQQATMPVLKHYKGVCHAYVDAGADLDQAVEIVFN 266 Query: 535 AKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL----NIPEA 590 K+ P CNA+E LLVHKD E A+L + L GVT P A +L Sbjct: 267 GKVQRPGVCNALECLLVHKD-EAAALLPAVAARLAPAGVTFRACPTALPLLGDAATAAAP 325 Query: 591 RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650 + E+ V VV+D+ A+ HI HGS HT+ I T DH A FLR+ D++ V Sbjct: 326 EDYGMEFHDLILAVRVVDDMDEALAHIAAHGSNHTEIICTRDHGRAMRFLREADASMVAV 385 Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 NASTRF+DG + GLGAE+G+ST ++H+ GP+GV+ L TT++++ G GQV Sbjct: 386 NASTRFNDGGQLGLGAEIGISTSKLHSYGPMGVQELTTTKFVVFGAGQV 434 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: 598 Number of extensions: 28 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: 436 Length adjustment: 36 Effective length of query: 681 Effective length of database: 400 Effective search space: 272400 Effective search space used: 272400 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