Align Delta-1-pyrroline-5-carboxylate synthase; P5CS; Aldehyde dehydrogenase family 18 member A1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_017597806.1 D471_RS0106100 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P54886 (795 letters) >NCBI__GCF_000341125.1:WP_017597806.1 Length = 424 Score = 255 bits (651), Expect = 4e-72 Identities = 151/416 (36%), Positives = 235/416 (56%), Gaps = 17/416 (4%) Query: 369 MARSGGRMLATLEPEQRA---EIIHHLADLLTDQRDEILLANKKDLEEAEGRLAAP-LLK 424 +A G L P RA + +AD L + DEI AN +D+E A P + Sbjct: 11 VAERAGDAAVDLAPLSRAVKDAALLAIADALVKRSDEITAANAEDVERARSEGTTPAFVD 70 Query: 425 RLSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIFESRP 484 RL+L+ ++ ++A +RQI D VG +R + L+L Q+ VP+GV+ +I+E RP Sbjct: 71 RLTLTPQRIEAVADAVRQIV-ELPDPVGESVRGGVLPNGLDLRQIRVPLGVIGIIYEGRP 129 Query: 485 DCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVK-EAVQLV--NTREE 541 + AAL + SGN LL+G A SN L + +EAL GV +AVQ+V TRE Sbjct: 130 NVTVDAAALCLKSGNAALLRGSSSAYSSNAALVSIMREALEGTGVPVDAVQMVPGRTRES 189 Query: 542 VEDLCRLDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVTRLV 601 L R ++D++IPRG + L++ + + + +PV+ EG+CH+YVD +A +DK + Sbjct: 190 STALMRARGLVDVLIPRGGNSLIQAVVRDST-VPVIETGEGLCHVYVDEDADLDKAVAIA 248 Query: 602 RDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQVKIHAGPKFASY-------L 654 ++K + + CNA ETLL+H + T L +++D L V +H + + Sbjct: 249 TNAKAQRCSVCNAAETLLVHEAVADTFL-PRVLDSLAEAGVTVHGDARVLAVSQAAGGSA 307 Query: 655 TFSPSEVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHV 714 T + + TEY ++L + VV + DA+ HI +Y + HT+ IVT+ + + +F+ V Sbjct: 308 TVVEATEEDWATEYLSMDLAVRVVPTIDDALAHIRRYSTRHTEAIVTDSLSASRYFVSRV 367 Query: 715 DSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRGKDHV 770 DSA V NASTRF+DG FG GAE+GIST ++HARGP+GL + +TK+++ G H+ Sbjct: 368 DSAAVMVNASTRFTDGGEFGFGAEIGISTQKLHARGPMGLTEMTSTKYVVTGDGHL 423 Lambda K H 0.319 0.135 0.387 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: 699 Number of extensions: 32 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 795 Length of database: 424 Length adjustment: 36 Effective length of query: 759 Effective length of database: 388 Effective search space: 294492 Effective search space used: 294492 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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