Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_028315042.1 G491_RS0114065 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000429905.1:WP_028315042.1 Length = 418 Score = 299 bits (766), Expect = 2e-85 Identities = 167/411 (40%), Positives = 259/411 (63%), Gaps = 11/411 (2%) Query: 297 DMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMV 356 DMA AAR +SR++ S + + K+L DIA L+ + + EN D+ +A+E+GL +M+ Sbjct: 9 DMAKAARAASREIGKCSGQVKDKVLTDIAALLKEEASFLYQENAKDLEAAKESGLSSAMI 68 Query: 357 ARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRP 416 RL + I S+A + ++A M DP+G ++K + +GL + K PLGV+ +++ESRP Sbjct: 69 DRLTIKEATIESMAQGLIEVAAMADPVGSMVKMWQRPNGLSVGKMRIPLGVVCMIYESRP 128 Query: 417 DALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDA-----IPETVGGKLIGLVTSR 471 + + A L +++GN ++L+GG EA SN L +VI A +PETV +L+ + T R Sbjct: 129 NVTIDAAGLCLKAGNAVVLRGGSEAIHSNRALGQVIAKALAKNGLPETV-VQLVPM-TDR 186 Query: 472 EEIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRI 531 E + +LL ++ IDLVIPRG L+ + + IPVL H G+CHVYVD++ D DMA I Sbjct: 187 EAVKELLTQEEYIDLVIPRGGEGLIRFVVANSSIPVLKHYKGVCHVYVDRSADHDMAVNI 246 Query: 532 VSDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL---NIP 588 + K+ P CNA+ETLLV+ + E A L ++ L +GV G P+ IL Sbjct: 247 CQNGKVQRPGVCNAVETLLVN-EAEAAAFLPKVCEVLSRDGVEFRGCPKTCAILKDAKPA 305 Query: 589 EARSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAV 648 + + E+ V+VV+D+ A+DHI ++GS HT+ IVT+++ A+ F R+VD++AV Sbjct: 306 QEEDWPAEFLDLILAVKVVKDMDEAMDHIAKYGSLHTETIVTDNYTRAKRFCREVDASAV 365 Query: 649 FHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 NASTRF+DG + GLGAE+G+ST ++HA GP+GVE L T++++ G+GQ+ Sbjct: 366 MVNASTRFNDGGQLGLGAEIGISTSKLHAFGPMGVEELTATKFVVEGQGQI 416 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: 632 Number of extensions: 25 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: 418 Length adjustment: 36 Effective length of query: 681 Effective length of database: 382 Effective search space: 260142 Effective search space used: 260142 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: 52 (24.6 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