Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate WP_043747100.1 AMB_RS20640 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >NCBI__GCF_000009985.1:WP_043747100.1 Length = 422 Score = 270 bits (691), Expect = 8e-77 Identities = 151/417 (36%), Positives = 238/417 (57%), Gaps = 7/417 (1%) Query: 292 DVSTREMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGY 351 D ++ AR +R L S + K L A A+ + LI + N D+ A + G Sbjct: 7 DALMTDLGQRARKAARILALTPSAAKDKALRAAAQAIRIDTKLILAANAKDMEAGEAKGL 66 Query: 352 EKPLVARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIV 411 K ++ RL + P ++ ++AK + +A + DP+ + L + + + + + + PLGV+ I+ Sbjct: 67 SKAMLDRLMLNPARVEAMAKGLEDIARLPDPVGRSLAEWTRPNGMSIARIAVPLGVIGII 126 Query: 412 FESRPDALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPR-NVGEKLIGLVTT 470 +ESRP+ A+L ++SGN +L+GG E+ S+ + + + + +V T Sbjct: 127 YESRPNVTADAAALCLKSGNATILRGGSESFHSSQAILTALKGGFTACGLPADAVQMVPT 186 Query: 471 RDEIAD--LLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMA 528 D A +L+L + ID+++PRG LV ++ A ++IP+ H +GICH Y+D SAD++MA Sbjct: 187 TDRAAVGVMLRLSNYIDVIVPRGGKSLVERVVAESRIPLFQHLEGICHTYVDGSADLEMA 246 Query: 529 KHIVMDAKIDYPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALG-- 586 K IV++AK+ C A ETLLV + L ++ L G + G +A A Sbjct: 247 KTIVLNAKMRRTGICGATETLLVDR-ACAGTHLAPLVAMLIDAGCEVRGDAVAQAADARV 305 Query: 587 FPKA-VSFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDS 645 P + + EY +V VD V +A++HI+ +GS HT+ IV D +VAETFL DS Sbjct: 306 IPASDADWSTEYLDAIISVGVVDGVGAAVEHINTHGSHHTEAIVAEDSQVAETFLNGCDS 365 Query: 646 AAVFHNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQVVNG 702 A V NAST+F+DG FG+GAE+GISTG++HARGPVGVE L T +++++G GQV G Sbjct: 366 AIVLWNASTQFADGGEFGMGAEIGISTGKMHARGPVGVEQLCTFKYVVKGNGQVRPG 422 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: 586 Number of extensions: 18 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: 422 Length adjustment: 36 Effective length of query: 680 Effective length of database: 386 Effective search space: 262480 Effective search space used: 262480 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: 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