Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_066918355.1 ACG33_RS02275 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_001579945.1:WP_066918355.1 Length = 427 Score = 262 bits (670), Expect = 2e-74 Identities = 149/407 (36%), Positives = 227/407 (55%), Gaps = 12/407 (2%) Query: 301 AARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLT 360 AA +R L SS + LL A A+ A D I + N D+ A G L+ RL Sbjct: 23 AAVQAARLLARASSASKDAALLGAAAAVRAQRDDILAANALDLRQAGERGLSAALLDRLA 82 Query: 361 IKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALV 420 + ++ ++A+ I +A + DP+ ++ E + L + + PLGV+ I++ESRP+ Sbjct: 83 LDDKRVEAMARGIEEIAALADPVGTVMASWERPNGLRIARVRVPLGVIGIIYESRPNVTA 142 Query: 421 QIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNVG--EKLIGLVTTRDEIADLL 478 +L ++SGN ++L+GG E+ S+ +H + + R G E I V T D A L Sbjct: 143 DAGALCLKSGNAVILRGGSESSHSSRAIHACLVSGL-REAGLPEAAIQRVPTTDRAAVGL 201 Query: 479 KLDDV---IDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDA 535 L + ID+++PRG LV +++ ++PV+GH +G CHVY+D+ AD DMA+ +V++A Sbjct: 202 LLSGMTQYIDVLVPRGGRSLVERVQREARVPVIGHLEGNCHVYVDRDADADMAREVVLNA 261 Query: 536 KIDYPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVS--- 592 K+ C A ET+L +D + G ++ AL G + G A + Sbjct: 262 KMRRTGICGAAETVLFDRDCPAAAG---VVAALLEAGCEVRGDEAVQALDARVVAANEQD 318 Query: 593 FHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNA 652 + EY + VD V+ A+ HI RYGS HT+ IVT + + AE FL VDSA V HNA Sbjct: 319 WMTEYLAPIIAARVVDTVEGAMAHIERYGSGHTESIVTGNPQTAERFLAGVDSAIVLHNA 378 Query: 653 STRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 ST+F+DG FG+GAE+GIST + HARGPVGVE L + ++++ G GQ+ Sbjct: 379 STQFADGGEFGMGAEIGISTDKFHARGPVGVEQLTSYKYVVHGSGQL 425 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: 605 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: 716 Length of database: 427 Length adjustment: 36 Effective length of query: 680 Effective length of database: 391 Effective search space: 265880 Effective search space used: 265880 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