Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_041456549.1 AVA_RS00285 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_000204075.1:WP_041456549.1 Length = 434 Score = 342 bits (878), Expect = 2e-98 Identities = 188/425 (44%), Positives = 267/425 (62%), Gaps = 8/425 (1%) Query: 294 STREMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEK 353 S ++A R + L LS+E + + + VA ALE+ ++ I N AD AA G K Sbjct: 9 SLNDIAQQTRQAASLLAMLSTEAKNQAIAAVAQALESAKEEILQANIADCEAATAEGIAK 68 Query: 354 PLVARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFE 413 PL RL + K+ +R + + DPI Q+ + E+ LVL++ +CPLGVL I+FE Sbjct: 69 PLYKRLQLDEHKLRDAIAGVRDVGKLADPIGQVQIQRELDTGLVLKRITCPLGVLGIIFE 128 Query: 414 SRPDALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPR-NVGEKLIGLVTTRD 472 +RP+A +QI SLAI+SGNG++LK GKEA+RS + K + + +V ++ L+TTR+ Sbjct: 129 ARPEAAIQIISLAIKSGNGVILKCGKEAVRSCEAIVKAVKQGLSTTDVNPDVVQLLTTRE 188 Query: 473 EIADLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIV 532 E +LL+LD +DL+IPRGSN V ++ +T+IPVLGHADGICHVYIDKSAD++ A + Sbjct: 189 ETLELLRLDKYVDLIIPRGSNSFVRFVQENTRIPVLGHADGICHVYIDKSADIEKAIAVS 248 Query: 533 MDAKIDYPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKAL---GFPK 589 +DAK+ YPAACNA+ETLLVH + + L + AL V + G + L Sbjct: 249 VDAKVQYPAACNAIETLLVHHSI-AAEFLPKVAQALAERQVELKGDERTLQILPEIAAAT 307 Query: 590 AVSFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVF 649 A+ + EYS +++ VD + AI HI++YGS HTD I+T D ETF V+SA VF Sbjct: 308 AIDWETEYSDFILSIKIVDSLTEAIAHINQYGSRHTDAIITEDVAAVETFFGLVNSAGVF 367 Query: 650 HNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVV---NGDKDV 706 HN STRF+DG R+G GAEVGIST ++ RGPVG+EGL+T ++ + G G +V G+ Sbjct: 368 HNCSTRFADGFRYGFGAEVGISTQQMPPRGPVGLEGLVTYKYQMTGTGHIVATYTGENAK 427 Query: 707 VYTHK 711 +TH+ Sbjct: 428 PFTHQ 432 Lambda K H 0.317 0.134 0.377 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: 665 Number of extensions: 27 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: 716 Length of database: 434 Length adjustment: 36 Effective length of query: 680 Effective length of database: 398 Effective search space: 270640 Effective search space used: 270640 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 09 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