Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate GFF503 Psest_0508 gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__psRCH2:GFF503 Length = 421 Score = 295 bits (754), Expect = 4e-84 Identities = 163/406 (40%), Positives = 243/406 (59%), Gaps = 8/406 (1%) Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360 AARE+SR L S+ + + L A AL+A + NELD+A + GL+ +M+ RL Sbjct: 15 AAREASRVLARASTAQKNRALQAAAAALDAARDELVRANELDLAGGRANGLDAAMLDRLA 74 Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420 +TP I + +R++A + DPIG + + G+ + K PLGV+ I++ESRP+ + Sbjct: 75 LTPKVIDGMIEGLRQVATLPDPIGAIRDMRYMPSGIQVGKMRVPLGVVGIIYESRPNVTI 134 Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET---VGGKLIGLVTSREEIPDL 477 ASL ++SGN +L+GG EA SN + + I + E + T R + L Sbjct: 135 DAASLCLKSGNATILRGGSEAIHSNQAIARCIQLGLAEAGLPAAAVQVVETTDRAAVGAL 194 Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537 + + + +D+++PRG L+ +I ++PV+ H DGICHVY+D A D D A RI +AK Sbjct: 195 ISMPEFVDVIVPRGGKGLIERISRDARVPVIKHLDGICHVYIDVAADVDKAIRIADNAKT 254 Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL--NIPEA--RSF 593 A CN METLLVH + + VL L + V L G PR +L ++ EA + Sbjct: 255 QRFAPCNTMETLLVHPGIAEQ-VLPPLAAIYREKSVELRGCPRTRALLGSDVLEASEEDW 313 Query: 594 NHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNAS 653 + EY A ++ +V+ + AI+HI+R+GS HTD IVTE+ A FL +VDSA+V NAS Sbjct: 314 STEYNAPILSIRLVDSLDAAIEHINRYGSQHTDAIVTENFTDARRFLTEVDSASVMINAS 373 Query: 654 TRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 TRF+DGF +GLGAE+G+ST ++HARGPVG+EGL + ++++ G G V Sbjct: 374 TRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTSEKYVVFGDGHV 419 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: 618 Number of extensions: 20 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: 421 Length adjustment: 36 Effective length of query: 681 Effective length of database: 385 Effective search space: 262185 Effective search space used: 262185 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