Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Dsui_1220 Dsui_1220 gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__PS:Dsui_1220 Length = 418 Score = 274 bits (700), Expect = 7e-78 Identities = 148/404 (36%), Positives = 240/404 (59%), Gaps = 7/404 (1%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 AR +SR++ + + + LL IA A+ + + A N D+A+A+ AGLE +MV RL + Sbjct: 14 ARAASRQMAKADTNAKNRALLAIAAAIRRDEAKLLAANGEDLAAARAAGLEPAMVDRLTL 73 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 +P ++++A + ++A + DPIG + G+ + PLGV+ I++E+RP+ V Sbjct: 74 SPKTVATMAEGLEQIASLPDPIGEMTDLRFRPSGIQVGHMRVPLGVIGIIYEARPNVTVD 133 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET---VGGKLIGLVTSREEIPDLL 478 A L I+SGN +L+GG EA R N L ++ + + + T R + +L+ Sbjct: 134 AAGLCIKSGNASILRGGSEAIRCNQALATLVKEGLQSAGLPADAVQVVETTDRAAVGELI 193 Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538 + + +D+++PRG L+ ++ +++P++ H DG CHVY+D + D A +V ++K Sbjct: 194 TMREFVDVIVPRGGKGLIARLLAESRVPMIQHLDGNCHVYLDDSADAAKAMAVVENSKTQ 253 Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL-NIPEARS--FNH 595 CN E+LLV + + +L + L + GV + G ++ N EA + Sbjct: 254 RYGTCNTAESLLVARSVAAT-LLPPIAAMLTAKGVEIRGCAETRALVPNAKEATEADWGE 312 Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655 EY A V+VV + AI+HI+++ S+HT+ IVTE+H A FLR+VDSA+V NASTR Sbjct: 313 EYLAPIIAVKVVAGLDEAIEHINKYSSSHTEAIVTENHTHAMRFLREVDSASVMVNASTR 372 Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 F+DGF +GLGAE+G+ST +IHARGPVG+EGL + +W++ G GQV Sbjct: 373 FADGFEYGLGAEIGISTDKIHARGPVGLEGLTSQKWVVLGNGQV 416 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: 547 Number of extensions: 15 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: 418 Length adjustment: 36 Effective length of query: 681 Effective length of database: 382 Effective search space: 260142 Effective search space used: 260142 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 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