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 207423 DVU1953 gamma-glutamyl phosphate reductase
Query= SwissProt::P54886 (795 letters) >MicrobesOnline__882:207423 Length = 419 Score = 279 bits (714), Expect = 2e-79 Identities = 163/414 (39%), Positives = 250/414 (60%), Gaps = 9/414 (2%) Query: 363 VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEA-EGRLAAP 421 +E G AR+ GR LA P +A + HLA LL ++D IL AN DL A E + AP Sbjct: 7 IEDMGRRARAAGRRLAAASPAAKAGALDHLATLLEQRQDAILAANAADLAAAAEAGMDAP 66 Query: 422 LLKRLSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIFE 481 + RL L+ + + +A R +AA D VG + + + L + ++ +P+GV+ +I+E Sbjct: 67 RMDRLRLTPATIAEMAAACRHVAALP-DPVGAIETQWQRPNGLLVGKMRIPLGVIAMIYE 125 Query: 482 SRPDCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVK-EAVQLVNT-- 538 SRP+ A L + +GN ++L+GG EA HSN L L EALS G+ EAVQ+V+T Sbjct: 126 SRPNVTIDSAILCLKAGNAVILRGGSEAIHSNLALAALITEALSSVGLPAEAVQVVSTTD 185 Query: 539 REEVEDLCRLDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVT 598 R + +LC+L++ ID+IIPRG L+R + A+ +PV+ H +G+CH Y+DS A + + Sbjct: 186 RAVIAELCKLEEHIDVIIPRGGETLIRAVVDMAR-MPVLKHYKGVCHAYIDSGADLAQAV 244 Query: 599 RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQVKIHAGPKFASYLTFS- 657 ++ ++K + P CNALE LL+HRD L I + L + V+ A P L S Sbjct: 245 EIIHNAKVQRPGVCNALEGLLVHRDEAAAFL-PAIAERLGNDGVEFRACPASLPLLGDSA 303 Query: 658 -PSEVKSLRTEYGDLELCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQHVDS 716 P + + E+ DL L + +VD++ +A+ HI YGS+HT++I T D A FL+ D+ Sbjct: 304 IPMKDEDNGQEFHDLILLVRIVDDMDEALAHIAAYGSNHTEIICTRDHGNAMRFLREADA 363 Query: 717 ACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRGKDHV 770 + V NAS+RF+DG + GLGAE+GISTS++H+ GP+G++ L TTK+++ G + Sbjct: 364 SMVAVNASSRFNDGGQLGLGAEIGISTSKLHSYGPMGVQELTTTKFVVFGAGQI 417 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: 748 Number of extensions: 26 Number of successful extensions: 5 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: 795 Length of database: 419 Length adjustment: 36 Effective length of query: 759 Effective length of database: 383 Effective search space: 290697 Effective search space used: 290697 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 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