Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate HSERO_RS02965 HSERO_RS02965 gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__HerbieS:HSERO_RS02965 Length = 422 Score = 273 bits (699), Expect = 1e-77 Identities = 152/407 (37%), Positives = 241/407 (59%), Gaps = 10/407 (2%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 AR +SR + + + + LL IA A+ + ++A N LD+ +A+ GL E+M+ RL + Sbjct: 15 ARAASRAMARADTAAKNQALLLIAAAIRRDADALRAANALDLEAARANGLAEAMLDRLTL 74 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 + I+++A + ++A + DPIG + G+ + + PLGV+ I++E+RP+ V Sbjct: 75 SDKAIATMAEGLEQIASLPDPIGEISNMKYRPTGIQVGQMRVPLGVIGIIYEARPNVTVD 134 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDLL 478 A L I+SGN +L+GG EA N L K++ + + + + + +V T R + L+ Sbjct: 135 AAGLCIKSGNATILRGGSEAIHCNQALAKLVKEGLAGAGLPEQAVQVVETTDRAAVGALI 194 Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538 + + +D+++PRG L+ ++ K+P++ H DGICHVY+D DT A + +AK Sbjct: 195 TMQEYVDVIVPRGGKGLIERLMKEAKVPMIKHLDGICHVYIDDKADTRKALDVAFNAKCH 254 Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL------NIPEARS 592 CN METLLV +++ A+L L + V L A++IL Sbjct: 255 RYGTCNTMETLLVARNIAA-AILPPLSELYRVKEVELRCDAEAAEILAGYPLLKAATEED 313 Query: 593 FNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNA 652 ++ EY A V+VV D+ AI+HI+RH S HT+ I+TED+ A FLR+VDSA+V NA Sbjct: 314 WDTEYLAPILAVKVVADMDEAIEHINRHSSQHTESIITEDYTRAMRFLREVDSASVMVNA 373 Query: 653 STRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 STRF+DGF +GLGAE+G+S ++HARGPVG+EGL + ++I+ G GQV Sbjct: 374 STRFADGFEYGLGAEIGISNDKLHARGPVGLEGLTSLKYIVLGNGQV 420 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: 564 Number of extensions: 21 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: 422 Length adjustment: 36 Effective length of query: 681 Effective length of database: 386 Effective search space: 262866 Effective search space used: 262866 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