Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_010966528.1 CA_RS16755 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_000008765.1:WP_010966528.1 Length = 418 Score = 291 bits (745), Expect = 4e-83 Identities = 154/400 (38%), Positives = 254/400 (63%), Gaps = 7/400 (1%) Query: 306 SRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLTIKPGK 365 ++ L + + K L++++ AL N+D I S+N+ D+ A+ G K L+ RLT+ + Sbjct: 18 AKKLSYADTNTKNKALIEMSKALLENKDYILSQNKIDIENAEKIGTSKALIDRLTLNDKR 77 Query: 366 IASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALVQIASL 425 I +A+++ ++++DPI +++K + D+L + + PLGV+ I++E+RP+ V A+L Sbjct: 78 ITDMAEALIKTSSLQDPIGEVIKMWKTPDELQIGQMRVPLGVIGIIYEARPNVTVDAAAL 137 Query: 426 AIRSGNGLLLKGGKEAIRSNTILHKVITDA-IPRNVGEKLIGL--VTTRDEIADLLKLDD 482 I+SGN ++L+GGKEAI SNT + K+I +A + + + I +T R+ + +++L+ Sbjct: 138 CIKSGNSVILRGGKEAINSNTAIAKIIKNAVVTAGLPDGSIEFIDITDRETVNVMMRLNG 197 Query: 483 VIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDAKIDYPAA 542 +ID++IPRG L+ + ++ +PV+ G CHVY+DK AD D A+ I+++AK+ PA Sbjct: 198 LIDVLIPRGGAGLIKSVVENSSVPVIETGTGNCHVYVDKYADFDKAERIIINAKLQRPAV 257 Query: 543 CNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALG--FPKA-VSFHHEYSS 599 CNAME+LLVHKD+ L I LK V I G K + P F E+ Sbjct: 258 CNAMESLLVHKDVAHE-FLPRISSKLKELKVQIRGCAATQKIVKDIVPATDEDFGKEFLD 316 Query: 600 MACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTRFSDG 659 + +V+ VD ++ AIDHI +Y + H++ I+T + A+ FL+ VD+AAV+ NASTRF+DG Sbjct: 317 LILSVKVVDSLEEAIDHIFKYSTKHSEAIITENYTNAQRFLKEVDAAAVYVNASTRFTDG 376 Query: 660 ARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 +FG G E+GIST ++HARGP+G+E L TT++++ G GQ+ Sbjct: 377 EQFGFGGEIGISTQKLHARGPMGLEQLTTTKYVIYGDGQI 416 Lambda K H 0.317 0.134 0.377 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: 640 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: 716 Length of database: 418 Length adjustment: 35 Effective length of query: 681 Effective length of database: 383 Effective search space: 260823 Effective search space used: 260823 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 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