Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_012283716.1 HM1_RS12290 gamma-glutamyl-phosphate reductase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_000019165.1:WP_012283716.1 Length = 417 Score = 265 bits (676), Expect = 4e-75 Identities = 145/406 (35%), Positives = 241/406 (59%), Gaps = 11/406 (2%) Query: 302 ARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLTI 361 A+D + L +LSS+ + K L +A AL A E+ I + N D+ A + G K L+ RL + Sbjct: 14 AKDAAYKLGSLSSQVKNKALEAMAYALVAQEEEILAANALDMEAGRQKGMSKALLDRLML 73 Query: 362 KPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALVQ 421 +I +A+ + L ++ DPI ++ ++ + L + + PLGV+ I++E+RP+ V Sbjct: 74 NKKRIEEMAEGLYALVSLPDPIGEVKRQWRRPNGLEIGQVRVPLGVVGIIYEARPNVTVD 133 Query: 422 IASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPR-NVGEKLIGLV--TTRDEIADLL 478 A L +++GN ++L+GG EAIRSN + K I+ A + E I LV ++R+ ++ Sbjct: 134 AAGLCLKTGNAVILRGGSEAIRSNMAIVKAISKASEEAGIPEGAIQLVEDSSREVAQQMM 193 Query: 479 KLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDAKID 538 +++ +D++IPRG L+ + + +PV+ G CH+Y+D AD++MA+ I+++AK Sbjct: 194 TMNEYLDVLIPRGGAGLIQAVVKNATVPVIETGVGNCHIYVDADADLEMAEKIIINAKCQ 253 Query: 539 YPAACNAMETLLVHKDLMKS--PGLDDILVALKTEGVNIYGGPIAHKALGFPKAVS---F 593 P CNA E+LLVH+D+ + P + +L + E + G P K + + Sbjct: 254 RPGVCNAAESLLVHQDVARKFIPHIGKVLTEMNVE---LRGCPRTLSLFSGIKEATDEDY 310 Query: 594 HHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNAS 653 E+ + V+ VD A++HI +Y + H++ IVT D A F RRVD+AAV+ NAS Sbjct: 311 ATEFLDLILAVKIVDSFDEALEHIRKYSTGHSEAIVTRDYSRAREFTRRVDAAAVYVNAS 370 Query: 654 TRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 TRF+DG +FG+GAE+GIST ++HARGP+G+ L T +++ G GQ+ Sbjct: 371 TRFTDGFQFGMGAEIGISTQKLHARGPMGLNELTTIKYVCYGDGQI 416 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: 599 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: 417 Length adjustment: 35 Effective length of query: 681 Effective length of database: 382 Effective search space: 260142 Effective search space used: 260142 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 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