Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate N515DRAFT_3773 N515DRAFT_3773 glutamate-5-semialdehyde dehydrogenase
Query= SwissProt::O04226 (716 letters) >FitnessBrowser__Dyella79:N515DRAFT_3773 Length = 420 Score = 293 bits (749), Expect = 2e-83 Identities = 152/409 (37%), Positives = 243/409 (59%), Gaps = 5/409 (1%) Query: 296 REMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPL 355 R A+A RD ++ L L++E ++ +L +ADAL A ++ N D+AAA+ G + + Sbjct: 5 RTQALACRDAAQVLAELTTEAKRALLQALADALHAGTGVVLEANARDMAAAREKGVQGAM 64 Query: 356 VARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESR 415 + RL + ++A + ++R +A + DP+ + ++ + L +E+ PLGV+ +++E+R Sbjct: 65 LDRLRLDEARVAGIVAALREVAALPDPVGVVTRRETRPNGLEVERVRVPLGVIAMIYEAR 124 Query: 416 PDALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIP-RNVGEKLIGLVTT--RD 472 P+ A+L + +GNG++L+GG EA+ SNT + V+ A+ + V E + LV+ R+ Sbjct: 125 PNVTADAAALCLMAGNGVILRGGSEAVHSNTAIAGVLRQALAAQGVPEAALTLVSDLRRE 184 Query: 473 EIADLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIV 532 + +LL+L D++DL IPRG L+ + ++PV+ H G+CH+Y+D++AD +A ++ Sbjct: 185 TMVELLQLSDIVDLAIPRGGEGLIRFVAEHARVPVIKHYKGVCHLYVDRAADQALALDLL 244 Query: 533 MDAKIDYPAACNAMETLLVHKDLMKS--PGLDDILVALKTEGVNIYGGPIAHKALGFPKA 590 +D K P CNA+ETLLVH+D+ P D L K E A+ Sbjct: 245 VDGKTSRPGVCNALETLLVHRDIAAEFLPRAADALGRRKVELRGCERSRALVPAMKPADE 304 Query: 591 VSFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFH 650 + EY + V VDD+++A+ HIHRY S HT+ I T D+ A F+R + SA V Sbjct: 305 TDYAAEYLDLILAVRIVDDLEAALAHIHRYSSDHTEVIATRDEDAARRFVRGIRSAVVMV 364 Query: 651 NASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 NAS+RFSDG GLGAE+GIST R+HA GP+G E L R+++RG GQV Sbjct: 365 NASSRFSDGGELGLGAEIGISTTRLHAYGPMGAEALTVERFVVRGDGQV 413 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: 576 Number of extensions: 24 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: 420 Length adjustment: 36 Effective length of query: 680 Effective length of database: 384 Effective search space: 261120 Effective search space used: 261120 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