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_092992235.1 BLP65_RS02485 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::P54886 (795 letters) >NCBI__GCF_900102855.1:WP_092992235.1 Length = 418 Score = 271 bits (694), Expect = 4e-77 Identities = 159/417 (38%), Positives = 247/417 (59%), Gaps = 16/417 (3%) Query: 363 VEQQGEMARSGGRMLATLEPEQRAEIIHHLADLLTDQRDEILLANKKDLEEAEGR-LAAP 421 ++Q G+ AR+ R +A + + +AD + QR ++L AN +DLE R L A Sbjct: 7 MQQVGQQARTASRAIARAGSNAKNAALTAIADAIEAQRPQLLKANSRDLEAGRERGLDAA 66 Query: 422 LLKRLSLSTSKLNSLAIGLRQIAASSQDSVGRVLRRTRIAKNLELEQVTVPIGVLLVIFE 481 LL RL L+ ++ +A GLRQIAA D VG + T +++ ++ VP+GV+ +I+E Sbjct: 67 LLDRLELNDERIAGMAEGLRQIAALP-DPVGEIADMTYRPSGIQVGKMRVPLGVIGIIYE 125 Query: 482 SRPDCLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGV-KEAVQLVNT-- 538 SRP+ AAL + SGN +L+GG EA HSN+ + E L G+ ++AVQ+VNT Sbjct: 126 SRPNVTADAAALCLKSGNAAILRGGSEAEHSNQAIAACIHEGLEKAGLPRDAVQVVNTTD 185 Query: 539 REEVEDLCRLDKMIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVT 598 R V +L + + +D+I+PRG L+ I A+ +PV+ H G+CH+Y+D +A DK Sbjct: 186 RAAVGELIAMPEYVDVIVPRGGKGLIERISADAR-VPVIKHLHGVCHVYIDDQADRDKAI 244 Query: 599 RLVRDSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQVKIHAGPKFASYLTFSP 658 ++ ++K + CN +ETLL+ D+ L ++ M + + V++ LT Sbjct: 245 QVAFNAKTQRYGTCNTMETLLVADDIAADVL-PELGAMFKEKGVELRGCEATRRILT--- 300 Query: 659 SEVKSLRTEYGDLE-----LCIEVVDNVQDAIDHIHKYGSSHTDVIVTEDENTAEFFLQH 713 ++ + E D E L I +V +++DAI+HIH++ S HT+ I+TE+ A FL Sbjct: 301 -DIVAATDEDWDAEYLAPILSIRIVRHMEDAIEHIHRHSSGHTESILTENIGRARRFLTE 359 Query: 714 VDSACVFWNASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRGKDHV 770 VDS+ V NASTRF+DG+ +GLGAE+GIST +IH RGPVGLEGL + K+++ G H+ Sbjct: 360 VDSSSVMVNASTRFADGFEYGLGAEIGISTDKIHVRGPVGLEGLTSQKYIVIGDGHI 416 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: 722 Number of extensions: 29 Number of successful extensions: 6 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: 418 Length adjustment: 36 Effective length of query: 759 Effective length of database: 382 Effective search space: 289938 Effective search space used: 289938 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