Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate 200302 SO1122 gamma-glutamyl phosphate reductase (NCBI ptt file)
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__MR1:200302 Length = 425 Score = 269 bits (688), Expect = 2e-76 Identities = 149/404 (36%), Positives = 241/404 (59%), Gaps = 11/404 (2%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 A+++S L L++ + +L IADAL N I A N DVA+A+ GL ++M+ RL++ Sbjct: 17 AKQASYALANLTASQKADLLDAIADALTENTLAILAANAKDVAAAKAEGLNDAMIDRLLL 76 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 +++ + + + + DP+G + +GL L + PLGV+ +++E+RP+ V Sbjct: 77 NESRLAGIIGDISDVVRLADPVGEEFGSRVLDNGLRLTRRRVPLGVIGVIYEARPNVTVD 136 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIP-ETVGGKLIGLVTSREE--IPDLL 478 IA LA+++GN ++L+GGKE SN ++ +VI AI + + + L+ S + + LL Sbjct: 137 IAVLALKTGNAVILRGGKETLESNKLISEVIRGAIASQGLPVDAVQLIDSSDRALVTGLL 196 Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538 KLD +D+++PRG L IPV+ GICH+YVDKA + + A ++++AK+ Sbjct: 197 KLDQYVDMIVPRGGQALQRLCAEQATIPVILGGIGICHLYVDKAANLERALEVIANAKVQ 256 Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN-------IPEAR 591 P CNA++TLLV K + N V +++ L GV ++ +L+ + + Sbjct: 257 RPTVCNALDTLLVDKTIAANFV-PQIVEYLHCLGVRFSVCEQSHALLDGLGFDIELATEQ 315 Query: 592 SFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHN 651 SF E+ + ++VV D+ AI HI RH S H++ I+T+D A F+ +V+SAAV+ N Sbjct: 316 SFATEWLSLTLGIKVVSDIDAAIAHIRRHSSGHSEAILTDDIHAATHFMNEVNSAAVYVN 375 Query: 652 ASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRG 695 ASTRF+DG +FGLGAEV VST ++HARGP+G+E L T +W+ G Sbjct: 376 ASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWLAWG 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: 597 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: 425 Length adjustment: 36 Effective length of query: 681 Effective length of database: 389 Effective search space: 264909 Effective search space used: 264909 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