Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate CA265_RS20850 CA265_RS20850 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >FitnessBrowser__Pedo557:CA265_RS20850 Length = 415 Score = 251 bits (640), Expect = 7e-71 Identities = 144/409 (35%), Positives = 237/409 (57%), Gaps = 16/409 (3%) Query: 302 ARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLTI 361 A+ SR L +LS E +L +A AL AN +LI +EN D+A + E P RL + Sbjct: 10 AQQASRTLISLSKETTDAVLTALAAALVANTELILAENGKDLAKMPI---EDPKYDRLKL 66 Query: 362 KPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALVQ 421 +IA +A ++ +A + P+ +I+ + + L ++K S PLGV+ +++E+RP+ Sbjct: 67 SRERIADIANDLKNVAGLSSPLGKIISDKTLENQLHIQKVSVPLGVVGVIYEARPNVTAD 126 Query: 422 IASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPRNV--GEKLIGLVTTRDEIADLLK 479 + SL ++GN +LKGG +A SN + KVI + +N + L L R LL Sbjct: 127 VFSLCFKTGNVAVLKGGSDAEFSNLAIAKVIHGVLDKNGINADILTLLPAERAATEALLN 186 Query: 480 LDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDAKIDY 539 +D++IPRGS L++ ++ ++KIPV+ GI H Y D++ D++ K I+ +AK Sbjct: 187 ARGFVDVLIPRGSQSLINYVRENSKIPVIETGAGIVHTYFDETGDLEKGKAIIFNAKTRR 246 Query: 540 PAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKAL--GFPKAV------ 591 + CN+++ +L++++ + L +L L V +Y +++AL +P + Sbjct: 247 VSVCNSLDCVLINQNRLTD--LPALLSPLADGNVELYADEKSYEALKVSYPAQLLNQASP 304 Query: 592 -SFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFH 650 F E+ S+ V+ V D+ A++HI Y S H++ I++ D FL VD+AAV+ Sbjct: 305 EHFGTEFLSLKLAVKIVADLTEALNHIADYSSKHSEAIISEDADNIAQFLNEVDAAAVYA 364 Query: 651 NASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 NAST F+DGA+FGLGAE+GIST ++HARGP+G+E L + +W++RG GQV Sbjct: 365 NASTGFTDGAQFGLGAEIGISTQKLHARGPMGLEELTSYKWVVRGDGQV 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: 605 Number of extensions: 31 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: 716 Length of database: 415 Length adjustment: 35 Effective length of query: 681 Effective length of database: 380 Effective search space: 258780 Effective search space used: 258780 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 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