Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate 7023725 Shewana3_0955 gamma-glutamyl phosphate reductase (RefSeq)
Query= SwissProt::O04226 (716 letters) >FitnessBrowser__ANA3:7023725 Length = 425 Score = 258 bits (660), Expect = 3e-73 Identities = 145/409 (35%), Positives = 233/409 (56%), Gaps = 9/409 (2%) Query: 296 REMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPL 355 +++ A+ S L NLS+ ++ +L +A+AL N I + N DVAAA+ G + Sbjct: 11 QQLGSQAKQASYALANLSAVQKADLLEAIAEALTQNTQAILAANAKDVAAAKAEGLNDAM 70 Query: 356 VARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESR 415 + RL + ++A + I + + DP+ + + + L L + PLGV+ +++E+R Sbjct: 71 IDRLLLNESRLAGIIGDIGDVVRLADPVGEEFGSRVLDNGLRLTRRRVPLGVIGVIYEAR 130 Query: 416 PDALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIP-RNVGEKLIGLVTTRDE- 473 P+ V IA LA+++GN ++L+GGKE + SN ++ +VI AI + + + L+ + D Sbjct: 131 PNVTVDIAVLALKTGNAVILRGGKETLESNKLISEVIRGAIASQGLPVDAVQLIDSPDRA 190 Query: 474 -IADLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIV 532 + LLKLD +D+++PRG L IPV+ GICH+Y+DK AD++ A ++ Sbjct: 191 LVTGLLKLDQYVDMIVPRGGQALQRLCAEQATIPVILGGIGICHLYVDKHADLERALEVI 250 Query: 533 MDAKIDYPAACNAMETLLVHKDLMKS--PGLDDILVALKTEGVNIYGGPIAHKALGFPKA 590 +AK+ P CNA++TLLV + + P + + L L LGF + Sbjct: 251 ANAKVQRPTVCNALDTLLVDTAVAERFVPQIAEYLHRLGVRFSVCEQSYALLDGLGFDIS 310 Query: 591 V----SFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSA 646 SF E+ S+ ++ V D+ +AI HI Y S H++ I+T D VA F+ V+SA Sbjct: 311 PATEQSFATEWLSLTLGIKVVSDIDTAIAHIRTYSSGHSEAILTDDIHVATHFMNEVNSA 370 Query: 647 AVFHNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRG 695 AV+ NASTRF+DG +FGLGAEV +ST ++HARGP+G+E L T +W+ G Sbjct: 371 AVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWLAWG 419 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: 603 Number of extensions: 29 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: 425 Length adjustment: 36 Effective length of query: 680 Effective length of database: 389 Effective search space: 264520 Effective search space used: 264520 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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