Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_010936977.1 DET_RS06615 gamma-glutamyl-phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000011905.1:WP_010936977.1 Length = 424 Score = 275 bits (702), Expect = 4e-78 Identities = 157/414 (37%), Positives = 243/414 (58%), Gaps = 12/414 (2%) Query: 297 DMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMV 356 + A A+ +SR L SS + L +IA L N I N D A+ AG+ +M+ Sbjct: 10 EKARLAKAASRPLSYASSAQKDAALKNIAACLLNNAPAILEANLKDQTEAKAAGMTAAML 69 Query: 357 ARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRP 416 RL++T ++ +A +A + DP+G + + +GLV+ K PLGV+ ++ESRP Sbjct: 70 DRLIITQSRLEGIAKDTLAIAALPDPVGEIFDMNTMPNGLVIGKKRVPLGVIAAIYESRP 129 Query: 417 DALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLVTSREE-- 473 + V IA+L +++GN ++L+GGKE SN IL ++I A+ E + + + + + E Sbjct: 130 NVTVDIAALCLKAGNAVILRGGKETIHSNTILARLIRQAVEEAGLPQEAVQFIENTEHSL 189 Query: 474 IPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVS 533 + LLKL D IDLVIPRG L++ +K + IPV+ G+ H+YVD + A I Sbjct: 190 VNHLLKLSDQIDLVIPRGGAGLISYVKQNSFIPVVAGGIGVVHIYVDADANIADAVNIAY 249 Query: 534 DAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN------- 586 ++K+ P CNAM+TLLVHKD+ A L + GV + A +IL Sbjct: 250 NSKVQRPTVCNAMDTLLVHKDIAA-AFLPVVAAEWSKAGVEIRADKTAMEILENASSCKL 308 Query: 587 IPEARS-FNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDS 645 IP A + E+ A V+VV+ + A+ HI R+GS HT+ IVT+++ ++ FL +VD+ Sbjct: 309 IPAAADDWGKEFLALVAAVKVVDSLDEALSHIARYGSGHTESIVTQNYTSSQRFLNEVDA 368 Query: 646 AAVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 AAV NASTRF+DG +FGLGAE+G+ST ++HARGP+G++ + + +WI+ G GQ+ Sbjct: 369 AAVMVNASTRFTDGSQFGLGAELGISTQKMHARGPMGLKEITSYKWIVYGNGQI 422 Lambda K H 0.318 0.135 0.378 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: 553 Number of extensions: 16 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: 717 Length of database: 424 Length adjustment: 36 Effective length of query: 681 Effective length of database: 388 Effective search space: 264228 Effective search space used: 264228 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