Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Pf1N1B4_2688 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2688 Length = 415 Score = 272 bits (695), Expect = 3e-77 Identities = 150/404 (37%), Positives = 241/404 (59%), Gaps = 6/404 (1%) Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360 AARE+SR + S+ + + L A+AL+A + A NELD+A+ + GLE +++ RL Sbjct: 7 AAREASRVIGRASTAQKNRALQAAANALDAARAELTAANELDLAAGRANGLEPALLERLA 66 Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420 +TP +I + +R++A + DP+G + + G+ + K PLGV+ I++ESRP+ + Sbjct: 67 LTPERIDGMIVGLRQVAALPDPVGAIRDMSYRPSGIQVGKMRVPLGVIGIIYESRPNVTI 126 Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDL 477 ASL ++SGN +L+GG EA SN + I + E + ++ +V T R + L Sbjct: 127 DAASLCLKSGNATILRGGSEAIHSNRAIAACIQRGLAEAGLPAAVVQVVETTDRAAVGAL 186 Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537 + + + +D+++PRG L+ ++ ++PV+ H DGICHVYV D A+RI +AK Sbjct: 187 ITMPEYVDVIVPRGGRGLIERVSRDARVPVIKHLDGICHVYVSAHADLPKAQRIAFNAKT 246 Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNH 595 C AMETLLV + + ++ L + L+ GV L G R I+ A ++ Sbjct: 247 YRYGICGAMETLLVDQAVAKD-FLPSMAAQLREKGVELRGCERTRAIIEAVAATEEDWHT 305 Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655 EY A ++ VV+ + AI+HI+++GS HTD IV+E+ F+ +VDS++V N T Sbjct: 306 EYLAPILSIRVVDGLDQAIEHINKYGSHHTDSIVSENLADTRRFVAEVDSSSVMINTPTC 365 Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 F+DGF +GLGAE+G+ST ++HARGPVG+EGL ++I+ G GQ+ Sbjct: 366 FADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYIVVGDGQL 409 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: 600 Number of extensions: 22 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: 415 Length adjustment: 35 Effective length of query: 682 Effective length of database: 380 Effective search space: 259160 Effective search space used: 259160 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