Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_057687245.1 ABB28_RS15340 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_001431535.1:WP_057687245.1 Length = 418 Score = 282 bits (722), Expect = 2e-80 Identities = 151/407 (37%), Positives = 250/407 (61%), Gaps = 7/407 (1%) Query: 299 AVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVAR 358 A A R + + L + +R +L +A ALE++ I + N D+AAA+ G ++ R Sbjct: 8 ARACRAAATVVAGLDTVQRTALLQSMAAALESHAGQILAANARDLAAARDKGIGSAMLDR 67 Query: 359 LTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDA 418 L + P ++ ++A+++R +A + DP+ Q+ + + + ++K PLGV+ +++E+RP+ Sbjct: 68 LMLDPPRLFAMAQALRDVAGLPDPVGQVTRDDVRPNGIRVQKVRVPLGVIAMIYEARPNV 127 Query: 419 LVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRN-VGEKLIGLVTT--RDEIA 475 + A+L +++GNG++L+GG EAI SNT + + A+P + V E + ++T R+ + Sbjct: 128 TAEAAALCLKAGNGVILRGGSEAIHSNTAIAAALGSALPAHGVPEAAVTVLTDLRREAML 187 Query: 476 DLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDA 535 +LL+L D+IDL IPRG L+ + ++PV+ H G+CH+++D SAD+D A +++D Sbjct: 188 ELLQLHDLIDLAIPRGGEGLIRFVAEHARVPVIKHYKGVCHLFVDASADIDQAIDLLVDG 247 Query: 536 KIDYPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVS--- 592 K P+ACN++ETLLVH+D+ + L AL GV + ++ L A + Sbjct: 248 KCSRPSACNSLETLLVHRDVA-AEFLPRAGQALAARGVELRADALSLPLLAGSTAATDED 306 Query: 593 FHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNA 652 + E+ + V+ VDD+++AI HI RY S HT+ I T D AE F+ + SA V NA Sbjct: 307 YAAEFLDLVIAVKVVDDLEAAITHIRRYTSDHTEVIATRDADHAERFIHALQSAVVMVNA 366 Query: 653 STRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 S+RFSDG + GLG+E+GIST R+HA GP+G+E L R+++RG GQV Sbjct: 367 SSRFSDGGQLGLGSEIGISTTRLHAYGPMGLEALTVERFVVRGEGQV 413 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: 589 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: 418 Length adjustment: 35 Effective length of query: 681 Effective length of database: 383 Effective search space: 260823 Effective search space used: 260823 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 Jul 25 2024. The underlying query database was built on Jul 25 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