Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_026596240.1 H035_RS0103780 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000421465.1:WP_026596240.1 Length = 421 Score = 291 bits (744), Expect = 6e-83 Identities = 163/406 (40%), Positives = 245/406 (60%), Gaps = 11/406 (2%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 AR ++R++ + + + L +A A+E+ ++ EN D+A+ +E GL +++ RL + Sbjct: 17 ARAAARQIGRADTGAKNRALTSVAAAIESGRHRLQQENARDLAAGRERGLSPALLDRLEL 76 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 T +I ++A +R++A + DP+G+V + G+ + + PLGV+ I++ESRP+ V Sbjct: 77 TDSRIDAMAQGLRQIAALPDPVGQVADLSYRPSGIQVGRMRVPLGVIGIIYESRPNVTVD 136 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPETVGGKLIGLV---TSREEIPDLL 478 A L +++GN +L+GG EA SN L I + + ET + V T R + LL Sbjct: 137 AAGLCLKAGNACILRGGSEAVHSNQALAACIREGLAETGLPETTVQVIETTDRAAVGALL 196 Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538 ++D +D++IPRG L+ +I ++IPV+ H DG+CHVY+D D+D A I +AK Sbjct: 197 QMDRHVDVIIPRGGKGLIERIVAESRIPVIKHLDGVCHVYIDDRADSDKAVAIACNAKTQ 256 Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEAR-----SF 593 CNAMETLLV + + VL L + GV L G IL P+ R + Sbjct: 257 RFGVCNAMETLLVAEGIAAQ-VLPPLAEKYREAGVELRGCAETRSIL--PDCRPADETDW 313 Query: 594 NHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNAS 653 EY A V VV D+ A+DHI R+GS HTD IVTED+ A FLR+VDS++V NAS Sbjct: 314 GAEYLAPILAVRVVADLDEAMDHIQRYGSGHTDAIVTEDYSRARRFLREVDSSSVMVNAS 373 Query: 654 TRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 TRF+DGF +GLGAE+G+ST ++HARGPVG+EGL T ++I+ G GQ+ Sbjct: 374 TRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTTQKFIVLGDGQI 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: 631 Number of extensions: 22 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: 421 Length adjustment: 36 Effective length of query: 681 Effective length of database: 385 Effective search space: 262185 Effective search space used: 262185 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 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