Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_074201687.1 BUQ81_RS07120 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_900141795.1:WP_074201687.1 Length = 418 Score = 280 bits (716), Expect = 1e-79 Identities = 151/409 (36%), Positives = 240/409 (58%), Gaps = 6/409 (1%) Query: 296 RDMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESM 355 + + ARE+SR L+ +S+ + L IAD + T++AEN D+ + + GL+ ++ Sbjct: 9 QQLGAQAREASRTLRRVSTAQKNAALQAIADEIARKRETLQAENARDLEAGRANGLDVAL 68 Query: 356 VARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESR 415 + RL ++ I ++ ++++A + D +G + G+ + K PLGV+ I++ESR Sbjct: 69 LDRLELSDKVIDTMIDGLKQIAQLPDLVGEITDMRMRPSGIQVGKMRVPLGVVGIIYESR 128 Query: 416 PDALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSRE 472 P+ V A+L ++SGN +L+GG EA SN L + I + + + + +V T R Sbjct: 129 PNVTVDAAALCLKSGNAAILRGGSEAIHSNRALAECIRTGVEQAGLPSATVQVVETTDRA 188 Query: 473 EIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIV 532 + +L+ + + +D++IPRG L+ +I ++PV+ H DGICHVY+D+ D D A ++ Sbjct: 189 AVGELITMPEYVDVIIPRGGKGLIERISRDARVPVIKHLDGICHVYIDRDADVDKAIKVA 248 Query: 533 SDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA-- 590 +AK CNAMETLLV D+ VL L GV L G R I++ A Sbjct: 249 FNAKTQRYGVCNAMETLLVDDDIAAT-VLPPLAKLYAEKGVELRGCERTRAIIDAKPATE 307 Query: 591 RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650 + EY ++ VV+DV A+DHI ++ S HT+ I+TE+ A FL +VDS++V Sbjct: 308 EDWASEYLGPILSIRVVDDVDAAMDHIAQYSSGHTESIITENFTTARRFLAEVDSSSVMV 367 Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 NASTRF+DGF +GLGAE+G+ST + HARGPVG+EGL + +WI+ G G + Sbjct: 368 NASTRFADGFEYGLGAEIGISTDKFHARGPVGLEGLTSQKWIVLGDGTI 416 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: 625 Number of extensions: 29 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: 418 Length adjustment: 36 Effective length of query: 681 Effective length of database: 382 Effective search space: 260142 Effective search space used: 260142 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 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