Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_013011161.1 DACET_RS09495 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000025725.1:WP_013011161.1 Length = 411 Score = 278 bits (712), Expect = 3e-79 Identities = 153/403 (37%), Positives = 250/403 (62%), Gaps = 6/403 (1%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 A+++S L ++++ + L IA+ LEAN IK EN D+ A+E GL ++++ RL + Sbjct: 9 AKKASYVLMNVNTDVKDSALSAIAEKLEANRVKIKNENLKDLDYARETGLSDALIDRLTL 68 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 +I + +V+ + DP+G+V+ + +GL + K PLGV+ I+FESRP+ + Sbjct: 69 DDKRIDGMIQAVKDIRSQVDPVGKVVDGYKRPNGLYITKVKVPLGVVGIIFESRPNVTID 128 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPETVGGKL-IGLV--TSREEIPDLL 478 A+L ++SGN +L+GGKEA SN L +++ +A+ E K + ++ T R + ++L Sbjct: 129 AAALCLKSGNVAILRGGKEAVHSNTYLGRLMKEAVAEAGLPKACVNIIEDTDRGLVMEML 188 Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538 K ID++IPRG L+ + IP++ H DGICHVY+DK D +MA I +AK Sbjct: 189 KAKGSIDIMIPRGGKALIEFCTEHSLIPLVKHDDGICHVYIDKFADIEMAVSIAVNAKCQ 248 Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNHE 596 CN METLLVH+ + + VL L A + V L G +++++ +A ++ E Sbjct: 249 RVGVCNTMETLLVHEAVAET-VLKRLEKAYGEHNVELRGCEHTAELISCKKAAEEDWSTE 307 Query: 597 YCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTRF 656 Y +V+VV + AI+HI+++GS H++ IVTE++ +E+FL VD+AAV+ NASTR+ Sbjct: 308 YLDYILSVKVVSSIDEAIEHINKYGSMHSESIVTENYTNSEMFLNMVDAAAVYVNASTRW 367 Query: 657 SDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 +DG FG+GAE+G+ST ++H RGP+G + L TT++ + G+GQ+ Sbjct: 368 TDGGEFGMGAEIGISTQKLHCRGPMGADDLTTTKYRIYGQGQI 410 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: 573 Number of extensions: 21 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: 411 Length adjustment: 35 Effective length of query: 682 Effective length of database: 376 Effective search space: 256432 Effective search space used: 256432 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