Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Ac3H11_704 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_704 Length = 426 Score = 274 bits (701), Expect = 6e-78 Identities = 154/413 (37%), Positives = 243/413 (58%), Gaps = 12/413 (2%) Query: 298 MAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVA 357 + + A+ +S + + + K L +A L NV ++ +N D+ A+ AGL E MV Sbjct: 13 LGLQAKTASALMAKAPAAIKNKALKALARLLRENVDALQIDNARDLERARAAGLAEPMVD 72 Query: 358 RLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPD 417 RL ++P + + A +LA M D IG +L + G+ + + P+GV +++ESRP+ Sbjct: 73 RLKLSPKVLETCAEGCEQLAAMPDIIGEILGMKQQPSGIRVGQMRVPIGVFGMIYESRPN 132 Query: 418 ALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEI 474 ++ ASL+I+SGN +L+GG EA SN L K++ A+ E + + LV T RE + Sbjct: 133 VTIEAASLSIKSGNACILRGGSEAIDSNKALAKLVQQALAEAGLPQDAVQLVQTTDREAV 192 Query: 475 PDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSD 534 L+ + +D++IPRG L+ +I K+PV+ H DG CH YVD CD MA ++ + Sbjct: 193 GQLIAMPQFVDVIIPRGGKGLIERISRDAKVPVIKHLDGNCHTYVDDPCDVPMAVKVADN 252 Query: 535 AKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN-------I 587 AK + + CNA E LLV + + L ++ + GV + G P + IL + Sbjct: 253 AKTNKYSPCNASEGLLVARGVAAE-FLPKIGAVYAAKGVEMRGCPESLAILQSVAGAQLV 311 Query: 588 PEA-RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSA 646 P + ++ EY A +V++V + AI HI+ + S HTD I+T +H A+ FLR+VDSA Sbjct: 312 PATEQDWSEEYLAPIISVKIVAGLDEAIAHINHYSSHHTDAILTTNHVHAQRFLREVDSA 371 Query: 647 AVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 +V NASTRF+DGF +GLGAE+G+ST + HARGPVG+EGL + ++++ G+G+V Sbjct: 372 SVMVNASTRFADGFEYGLGAEIGISTDKFHARGPVGIEGLTSLKYVVLGEGEV 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: 586 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 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