Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_086508696.1 BZY95_RS04055 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_002151265.1:WP_086508696.1 Length = 433 Score = 286 bits (731), Expect = 2e-81 Identities = 157/407 (38%), Positives = 245/407 (60%), Gaps = 11/407 (2%) Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360 AAR ++ +++ + D+ + LL +A L+ + I N D+A + +GLE +++ RL Sbjct: 28 AARVAATQMRRAVTGDKNRALLAMAAHLQRRRSEILEANAADLARGRASGLEAALLDRLA 87 Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420 + +I ++ + ++A + DP+G + G+ + + PLGV+ I++ESRP+ + Sbjct: 88 LNDARIDAMIEGLEQVAALPDPVGEIEGLRYRPSGIQVGQMRVPLGVIGIIYESRPNVTM 147 Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAI-----PETVGGKLIGLVTSREEIP 475 + ASL ++SGN +L+GG EAR SNA + I D + PET + T R + Sbjct: 148 EAASLCLKSGNASILRGGSEARDSNAAIAACIRDGLRDAGLPETA--VQVVATTDRAAVG 205 Query: 476 DLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDA 535 L+ + + +D++IPRG L+ +I ++PV+ H DG+CHVY+D D + A I +A Sbjct: 206 QLIAMPEYVDVIIPRGGKSLIERISREARVPVIKHLDGVCHVYIDATADPEKALAIAVNA 265 Query: 536 KLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEARS--- 592 K CN METLLV + + A+L L A ++GV L G R+ IL+ A S Sbjct: 266 KTHRYGTCNTMETLLVDAPVAE-ALLPRLAQAYAAHGVELRGCERSRAILDDIAAASEED 324 Query: 593 FNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNA 652 + EY A V VV+ + AI+HI R+GS HTD IVTED+ +A F+ +VDS++V NA Sbjct: 325 WYAEYLAPVLAVRVVDGMEAAIEHIERYGSHHTDAIVTEDYGLARRFMAEVDSSSVMVNA 384 Query: 653 STRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 STRF+DGF +GLGAE+G+ST ++HARGPVG+EGL T ++++ G GQV Sbjct: 385 STRFADGFEYGLGAEIGISTDKLHARGPVGLEGLTTRKYVVLGDGQV 431 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: 624 Number of extensions: 26 Number of successful extensions: 4 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: 433 Length adjustment: 36 Effective length of query: 681 Effective length of database: 397 Effective search space: 270357 Effective search space used: 270357 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