Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate RR42_RS17530 RR42_RS17530 gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Cup4G11:RR42_RS17530 Length = 426 Score = 266 bits (681), Expect = 1e-75 Identities = 149/412 (36%), Positives = 236/412 (57%), Gaps = 18/412 (4%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 AR +SR + S+ D+ + LL IA A+ + +KA N DV A+ G + + + RL + Sbjct: 17 ARAASRAMARASTADKNRALLTIAAAIRRDAAHLKAVNAGDVERARANGQDAAFIDRLTL 76 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 + I ++AA + ++A + DPIG + G+ + + PLGV+ I++ESRP+ + Sbjct: 77 SDKAIDTMAAGLEQIAALADPIGEISNMKFRPTGIQVGQMRVPLGVIGIIYESRPNVTID 136 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAI------PETVGGKLIGLVTSREEIP 475 A+L ++SGN +L+GG EA SN L ++ + + PE V + T R + Sbjct: 137 AAALCLKSGNATILRGGSEAIDSNTALAALVAEGLAAAGLPPEAVQ---VISTTDRAAVG 193 Query: 476 DLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDA 535 L+ + + +D+++PRG L+ ++ ++P++ H DGICHVY+D D D A R+ +A Sbjct: 194 RLVTMTEYVDVIVPRGGKSLIARLMAEARVPMIKHLDGICHVYIDVDADLDKAVRVADNA 253 Query: 536 KLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLY------GGPRASKILNIPE 589 K A CN METLLV + + A L L Q GV L A+ + + Sbjct: 254 KTQRYAPCNTMETLLVARAVAA-AALPPLCRIYQEKGVELRVCAATRATLEAAGFTGLVD 312 Query: 590 A--RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAA 647 A + EY A + V + AI+HI+ +GSAHTD I+TE++ FLR+VDSA+ Sbjct: 313 ATEEDWRLEYLAPVLAIRTVAGLDEAIEHINTYGSAHTDSIITENYTTGMRFLREVDSAS 372 Query: 648 VFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 V NASTRF+DGF +GLGAE+G+S ++HARGPVG+EGL + ++++ G G++ Sbjct: 373 VMINASTRFADGFEYGLGAEIGISNDKLHARGPVGLEGLTSLKYVVFGHGEI 424 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: 576 Number of extensions: 24 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: 426 Length adjustment: 36 Effective length of query: 681 Effective length of database: 390 Effective search space: 265590 Effective search space used: 265590 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