Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate BPHYT_RS16770 BPHYT_RS16770 gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__BFirm:BPHYT_RS16770 Length = 423 Score = 270 bits (691), Expect = 8e-77 Identities = 150/418 (35%), Positives = 241/418 (57%), Gaps = 12/418 (2%) Query: 292 DSNARDMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGL 351 D D+ AR++SR + S+ + L +A +E + +K N DVA A+E G Sbjct: 4 DQYMTDLGRRARQASRAMARASTAAKNAALAAVAQGIERDAALLKEANARDVARAREKGH 63 Query: 352 EESMVARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIV 411 + + + RL ++ + ++ +R++A + DPIG + G+ + + PLGV+ I+ Sbjct: 64 DAAFIDRLTLSDKALKTMVEGLRQVAALADPIGEISNLKYRPSGIQVGQMRVPLGVIGII 123 Query: 412 FESRPDALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLVTS 470 +ESRP+ + A+L ++SGN +L+GG EA NA L K+I + + + + + + +V + Sbjct: 124 YESRPNVTIDAAALCLKSGNATILRGGSEALECNAALAKLIGEGLEKAGLPQEAVQVVAT 183 Query: 471 --REEIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMA 528 R + L+ + + +D+++PRG L+ ++ N ++P++ H DGICHVYVD D A Sbjct: 184 SDRAAVGKLITMTEYVDVIVPRGGKSLIERLMNEARVPMIKHLDGICHVYVDDRADLAKA 243 Query: 529 KRIVSDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN-- 586 + +AK CN METLLV + + VL L + V L A +L Sbjct: 244 LTVCDNAKTHRYGTCNTMETLLVARGIAAE-VLPPLGKLYRDKQVELRVDAAARAVLADA 302 Query: 587 ----IPEA--RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFL 640 + +A + EY A ++VVE++ AIDHI+ + S HTD IVTEDH+ A FL Sbjct: 303 GVGPLVDATEEDWRTEYLAPVLAIKVVENLDAAIDHINTYSSQHTDAIVTEDHDRAMRFL 362 Query: 641 RQVDSAAVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698 R+VDSA+V NASTRF+DGF FGLGAE+G+S ++HARGPVG+EGL + ++++ G G+ Sbjct: 363 REVDSASVMVNASTRFADGFEFGLGAEIGISNDKLHARGPVGLEGLTSLKYVVLGHGE 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: 598 Number of extensions: 31 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: 423 Length adjustment: 36 Effective length of query: 681 Effective length of database: 387 Effective search space: 263547 Effective search space used: 263547 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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