Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate 6938396 Sama_2515 gamma-glutamyl phosphate reductase (RefSeq)
Query= SwissProt::O04226 (716 letters) >FitnessBrowser__SB2B:6938396 Length = 420 Score = 252 bits (644), Expect = 2e-71 Identities = 144/406 (35%), Positives = 232/406 (57%), Gaps = 12/406 (2%) Query: 297 EMAVAARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLV 356 ++ AA+ L NL + ++L VA L++ D I + N DVAAA+ +G +V Sbjct: 9 QLGQAAKSSGFALANLGVMAKNRLLGRVAAELKSAFDEILAANAKDVAAARASGLGDAMV 68 Query: 357 ARLTIKPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRP 416 RL + ++ + I + ++ DPI + + + + L + PLGV+ +++E+RP Sbjct: 69 DRLLLNDDRLKGIIADIDNVISLADPIGEEFDSRLLDNGMRLCRRRVPLGVIGVIYEARP 128 Query: 417 DALVQIASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIP-RNVGEKLIGLVTTRDE-- 473 + V+IA LA+++GN ++L+GGKE + SN L I A+ + E + L+ D Sbjct: 129 NVTVEIAVLALKTGNAVILRGGKETLESNLALAAAIRRALAGEGLPEDCVQLIDNPDRAL 188 Query: 474 IADLLKLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVM 533 + LLKLD +D+++PRG L IPV+ GICH+Y+D+ AD+ A ++++ Sbjct: 189 VTGLLKLDKFVDMIVPRGGQGLQRLCAEQATIPVILGGIGICHLYLDRDADISRAANVII 248 Query: 534 DAKIDYPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYG-----GPIAHKALGFP 588 +AK+ P CNA++TLL+H+D K L + AL+ +GV + G +A + Sbjct: 249 NAKVQRPTVCNALDTLLIHRD--KLDWLPTLARALQQQGVKLVACEQSLGALAAAGIEAE 306 Query: 589 KAV--SFHHEYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSA 646 A SF E+ S+ V+ V D+ AI HI Y S H++ I+T + A F+ V+SA Sbjct: 307 AASDESFGTEWLSLTLGVKVVADIDEAIAHIRHYSSGHSEAILTDNLAAATHFMNEVNSA 366 Query: 647 AVFHNASTRFSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWI 692 AV+ NASTRF+DG +FG GAEV +ST ++HARGP+G+E L T +W+ Sbjct: 367 AVYLNASTRFTDGGQFGFGAEVAVSTQKLHARGPMGLEALTTYKWL 412 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: 624 Number of extensions: 30 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