Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Ga0059261_2506 Ga0059261_2506 glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41)
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Korea:Ga0059261_2506 Length = 422 Score = 279 bits (713), Expect = 2e-79 Identities = 159/408 (38%), Positives = 230/408 (56%), Gaps = 9/408 (2%) Query: 297 DMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMV 356 ++ AR ++ L L + + + L A A+ A+ I A N DVA+ + GL +++ Sbjct: 15 ELGARARAAAVTLAGLPAPAKAQGLRAAAAAIRADADAILAANARDVAAGEANGLSGALL 74 Query: 357 ARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRP 416 RL + P ++ AA V +A + DP+G V+ +E +GL L + P+GV+ I++ESRP Sbjct: 75 DRLRLDPARLEGAAAGVEAVAALADPVGEVISTSERPNGLQLSRVRVPIGVIGIIYESRP 134 Query: 417 DALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREE 473 + A+L + SGN +L+GG EA SN +H + + + + LV T R Sbjct: 135 NVTADAAALCVMSGNAAILRGGSEAVHSNRAIHAAFACGLADAGLPEDAVQLVPTTDRAA 194 Query: 474 IPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVS 533 + +LK D IDLV+PRG LV +++ ++PVL H DGI H Y+D A D DMA+ + Sbjct: 195 VGAMLKADGAIDLVVPRGGKSLVARVQEEARVPVLAHLDGINHTYIDGAADPDMARDLAV 254 Query: 534 DAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKI---LNIPEA 590 +AK+ C A ETLL+ A ++ AL G L G I + A Sbjct: 255 NAKMRRTGICGATETLLIDTAFADPA---PILSALADTGCELRGDADIRAIDPRVVAANA 311 Query: 591 RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650 ++ EY +V+ V+ V GA+ HI HGS HTD IVT D AE FL VDSA V Sbjct: 312 EDWDTEYLDSILSVKRVDGVVGAMAHIAAHGSHHTDAIVTGDAATAERFLNGVDSAIVMW 371 Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698 NAST+F+DG FGLGAE+G++TGR+HARGPV +EGL T +W++RG GQ Sbjct: 372 NASTQFADGGEFGLGAEIGIATGRLHARGPVALEGLTTYKWVVRGTGQ 419 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: 597 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: 422 Length adjustment: 36 Effective length of query: 681 Effective length of database: 386 Effective search space: 262866 Effective search space used: 262866 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 09 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