Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_012971337.1 ALVIN_RS10685 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000025485.1:WP_012971337.1 Length = 424 Score = 300 bits (768), Expect = 1e-85 Identities = 163/411 (39%), Positives = 248/411 (60%), Gaps = 11/411 (2%) Query: 297 DMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMV 356 D+ AR +SR+L S+ + LL IA+ L+A I A N D+ + GL+ +++ Sbjct: 15 DLGQRARAASRRLARASTAAKNSALLAIAERLDAERAAIAAANRRDLEAGAAKGLDAALL 74 Query: 357 ARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRP 416 RL +TPG+I ++ VR++A + DP+G + G+ + + PLGV+ I++ESRP Sbjct: 75 DRLELTPGRIDAMIEGVRQVAALPDPVGAITDLDYRPSGIQVGRMRVPLGVVGIIYESRP 134 Query: 417 DALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVI-----TDAIPETVGGKLIGLVTSR 471 + A+L ++SGN +L+GG EA SN + + I + +PE G + T R Sbjct: 135 NVTADAAALCLKSGNATVLRGGSEAFASNQAIARCIQAGLASAGLPED--GVQVVATTDR 192 Query: 472 EEIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRI 531 + ++ + + ID++IPRG L+ +I ++PV+ H DGICHVY+D+ D D A I Sbjct: 193 AAVGAMIAMPESIDVIIPRGGKGLIERISREARVPVIKHLDGICHVYIDEHADLDKAFAI 252 Query: 532 VSDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL--NIPE 589 +AK CN METLLV + + A+L L A + GV L G PR +++ +P Sbjct: 253 AMNAKTQRYGTCNTMETLLVDAPVAE-AILPRLAAAYREKGVELRGCPRTRELIVDAVPA 311 Query: 590 A-RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAV 648 ++ EY A ++ VV+ + A+DHI RHGSAHTD IVTED+ A FLR+VDS++V Sbjct: 312 TDEDWDTEYLAPVLSIRVVDGLDAAMDHITRHGSAHTDAIVTEDYSRARRFLREVDSSSV 371 Query: 649 FHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 NASTRF+DGF +GLGAE+G+ST + HARGPVG+EGL + ++++ G G+V Sbjct: 372 MVNASTRFADGFEYGLGAEIGISTDKFHARGPVGLEGLTSVKFVVLGDGEV 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: 626 Number of extensions: 25 Number of successful extensions: 4 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