Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_013430065.1 CALKRO_RS05450 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_000166775.1:WP_013430065.1 Length = 419 Score = 270 bits (689), Expect = 1e-76 Identities = 149/413 (36%), Positives = 241/413 (58%), Gaps = 11/413 (2%) Query: 297 EMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLV 356 E A ++ S+ + N+S E+ + L ++ + D I EN+ D+ A G + L+ Sbjct: 6 EKAKKVKEASKKIMNISENEKNRALSCISQKILEKMDFILQENQKDMENAVSKGIKGALL 65 Query: 357 ARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRP 416 RL + +I + K I + + DP+ +++ + + L++ + P+G + I++E+RP Sbjct: 66 DRLKLTEDRIKQICKGIEDVIKLPDPVGEVISMWKRPNGLLIGQKRVPIGAIGIIYEARP 125 Query: 417 DALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDA-IPRNVGEKLIGLV--TTRDE 473 + V A L +++GN +LL+GG EAI SN L KV+ + I + E I +V T+R+ Sbjct: 126 NVTVDAAVLCLKAGNSVLLRGGSEAINSNIALVKVMKEGLIEAGIEESSIEIVEDTSRET 185 Query: 474 IADLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVM 533 ++KL++ +DL+IPRG L+ + + +PV+ G CHV++D+SAD +MAK IV+ Sbjct: 186 AVAMMKLNEYLDLLIPRGGANLIKTVVQNATVPVIETGVGNCHVFVDESADFEMAKEIVI 245 Query: 534 DAKIDYPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKA-------LG 586 +AK P CNA E LLVH+++ + L IL L V I G + + + Sbjct: 246 NAKTQRPGVCNAAEKLLVHRNIAEE-FLPMILKELMERNVEIRGCSLTAEICRKNGIEIK 304 Query: 587 FPKAVSFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSA 646 ++ EY + V+ VD + AI+HI++YGS H++ IVT D A+ FL VD+A Sbjct: 305 LATEEDWYTEYLDLIMGVKVVDSIDDAIEHINKYGSKHSEAIVTKDYFNAQKFLDYVDAA 364 Query: 647 AVFHNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 AV+ NASTRF+DG FG GAE+GIST ++HARGP+G++ L T ++I+ G GQV Sbjct: 365 AVYVNASTRFTDGFEFGFGAEIGISTQKLHARGPMGLKELTTIKYIIYGSGQV 417 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: 604 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: 419 Length adjustment: 36 Effective length of query: 680 Effective length of database: 383 Effective search space: 260440 Effective search space used: 260440 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 Jul 26 2024. The underlying query database was built on Jul 25 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