Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_043880593.1 AZC_RS21220 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000010525.1:WP_043880593.1 Length = 437 Score = 265 bits (678), Expect = 3e-75 Identities = 151/408 (37%), Positives = 233/408 (57%), Gaps = 8/408 (1%) Query: 298 MAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVA 357 M AAR ++R L +E + L A + A I A N D+A A+ G+ + Sbjct: 28 MGRAARAAARTLALAPAEQKTAALKAAAARIRAATPEILAANADDMARARADGMSGAFQD 87 Query: 358 RLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPD 417 RL +T +I ++AA V +A + DP+G V + +GLV+E+ +PLGV+ +++ESRP+ Sbjct: 88 RLALTESRIEAIAAGVEMVAGLPDPVGAVTESWTRPNGLVIERVRTPLGVIGVIYESRPN 147 Query: 418 ALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEI 474 A+L +R+GN ++L+GG ++ S+ +HK + + + + V + R + Sbjct: 148 VTADAAALCVRAGNAVILRGGSDSLGSSGAIHKAFVAGLVDAGLSADCVQFVPFSDRTAV 207 Query: 475 PDLLK-LDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVS 533 +L LD +D+++PRG LV ++++ ++PV H DGI HVYV A D DMAK ++ Sbjct: 208 GLMLGGLDGNLDVIVPRGGKGLVARVQSEARVPVFAHLDGIVHVYVHAAADLDMAKTVLL 267 Query: 534 DAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKI---LNIPEA 590 +AK+ C A ETLLV + + + L L+ L G + G A + + Sbjct: 268 NAKMRRTGICGAAETLLVDEKVAASQ-LKPLVEMLLDAGCEVRGDAAAQAVDPRVKPAVD 326 Query: 591 RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650 ++ EY +V++V D+ AIDHI HGS HTD I+T D A FLR+VDSA V H Sbjct: 327 ADWDTEYEDAIISVKLVPDLAAAIDHIETHGSHHTDSIITRDEAAAARFLREVDSAIVMH 386 Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698 NAST+F+DG FG GAE+G++TGR+HARGPVG E L + ++ + G GQ Sbjct: 387 NASTQFADGGEFGFGAEIGIATGRMHARGPVGAEQLTSFKYRVHGNGQ 434 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: 603 Number of extensions: 24 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: 437 Length adjustment: 36 Effective length of query: 681 Effective length of database: 401 Effective search space: 273081 Effective search space used: 273081 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 Jul 25 2024. The underlying query database was built on Jul 25 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