Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_038140418.1 Q394_RS0103570 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000621325.1:WP_038140418.1 Length = 412 Score = 278 bits (710), Expect = 5e-79 Identities = 154/405 (38%), Positives = 242/405 (59%), Gaps = 9/405 (2%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 A+++++ L + + LL IA+ + +KAEN D+A+ +E GL+ +M+ RL + Sbjct: 8 AKQAAQVLANTDTSIKNNALLRIAEVILERADWLKAENAKDLAAGREKGLDAAMLDRLTL 67 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 + ++ +A VR++A + DPIG + + G+ + K PLGV+ I++ESRP+ V Sbjct: 68 SDKTLAGMAEGVRQVATLADPIGTITDLSYRPSGIQVGKMRVPLGVVGIIYESRPNVTVD 127 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPETVG--GKLIGLV--TSREEIPDL 477 A+L ++SGN +L+GG EA SN + + + E G + +V T R + +L Sbjct: 128 AAALCLKSGNATILRGGSEAIHSNQAIAACVRAGL-EAAGLPAACVQVVETTDRAAVGEL 186 Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537 L++ +D+++PRG L+ ++ ++IPV+ H DGICHVY+D D D A +I +AK Sbjct: 187 LRMAQYVDVIVPRGGKSLIERVSAESRIPVIKHLDGICHVYIDDQADLDKAVKIAVNAKT 246 Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILN--IPEARS-FN 594 CNAMETLLV + + VL L + GV L G + +L +P ++ Sbjct: 247 HRYGVCNAMETLLVAEGVAAQ-VLPALAEEYAAKGVELRGCEQTRALLPACVPATEEDWS 305 Query: 595 HEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNAST 654 EY A + VV D+ AI HI+ + S HTD I+TE++ A FLRQVDS++V NAST Sbjct: 306 TEYLAPILAIRVVADMVAAITHINTYSSQHTDAIITENYTRARAFLRQVDSSSVMVNAST 365 Query: 655 RFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 RF+DGF +GLGAE+G+ST +IHARGPVG+EGL + ++++ G G + Sbjct: 366 RFADGFEYGLGAEIGISTDKIHARGPVGLEGLTSQKYVVLGDGHI 410 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: 590 Number of extensions: 19 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: 412 Length adjustment: 35 Effective length of query: 682 Effective length of database: 377 Effective search space: 257114 Effective search space used: 257114 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