Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate YP_004140424.1 Mesci_1211 gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000185905.1:YP_004140424.1 Length = 428 Score = 270 bits (689), Expect = 1e-76 Identities = 143/410 (34%), Positives = 248/410 (60%), Gaps = 8/410 (1%) Query: 297 DMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMV 356 D+ AR ++R L ++ + LL +A+A+ A I N +DV++ E+GL S + Sbjct: 18 DIGRRARAAARPLAIATTAAKNAALLAMAEAIVAREQDILDANAIDVSNGHESGLSTSFM 77 Query: 357 ARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRP 416 RL + P +I ++A +R++A + DP+G V+ + + +GL +E+ +PLGV+ +++ESRP Sbjct: 78 DRLKLDPARIRAMADGIREIAALRDPVGDVIAQWDRPNGLHIERVRTPLGVVGVIYESRP 137 Query: 417 DALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREE 473 + +L +++GN ++L+GG ++ S+A +H + + + + + I LV T R Sbjct: 138 NVTADAGALCLKAGNPVILRGGSDSLNSSAAIHACLVEGLKQAGLPEDAIQLVPTTDRAA 197 Query: 474 IPDLLK-LDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIV 532 + ++LK L +D++IPRG LV +++ ++PV H +GICH+Y+D++ DMA RI Sbjct: 198 VGEMLKGLGGNLDVIIPRGGKSLVGRVQAEARVPVFAHLEGICHLYIDRSAKLDMAVRIA 257 Query: 533 SDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEARS 592 +AK+ C A ETLLV + + ++ ++ AL++ G ++ K+ + + Sbjct: 258 VNAKMRRTGVCGAAETLLVDRAVASTHLV-PILDALRAAGCEIHADAEVLKVFFDAKPAT 316 Query: 593 ---FNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVF 649 + EY V++V+ + GAI+HI S HT+ IV ED + E F ++DSA + Sbjct: 317 DADWVTEYLDAIIAVKLVDGIGGAIEHIETFSSHHTEAIVAEDAQAVERFFNEIDSAILL 376 Query: 650 HNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 HNAST+F+DG FG+GAE+G++TG++HARGPVGVE L + ++ +RG GQV Sbjct: 377 HNASTQFADGGEFGMGAEIGIATGKMHARGPVGVEQLTSFKYRVRGSGQV 426 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: 644 Number of extensions: 28 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: 428 Length adjustment: 36 Effective length of query: 681 Effective length of database: 392 Effective search space: 266952 Effective search space used: 266952 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