Align Delta-1-pyrroline-5-carboxylate synthase 1; OsP5CS1; EC 2.7.2.11; EC 1.2.1.41 (characterized)
to candidate 5210587 Shew_3015 gamma-glutamyl phosphate reductase (RefSeq)
Query= SwissProt::O04226 (716 letters) >FitnessBrowser__PV4:5210587 Length = 415 Score = 256 bits (653), Expect = 2e-72 Identities = 140/404 (34%), Positives = 230/404 (56%), Gaps = 7/404 (1%) Query: 302 ARDCSRHLQNLSSEERKKILLDVADALEANEDLIRSENEADVAAAQVAGYEKPLVARLTI 361 A ++ L + ++ + ILLD+A +L N IRS N D+A+A+ AG ++ RLT+ Sbjct: 11 AAQAAKTLAQVDTQTKNTILLDMARSLRDNSFEIRSANLIDLASAEQAGLSHAMIDRLTL 70 Query: 362 KPGKIASLAKSIRTLANMEDPINQILKKTEVADDLVLEKTSCPLGVLLIVFESRPDALVQ 421 +I ++A I +A + DPI + + L + K PLGV+ +++E+RP+ Sbjct: 71 DGDRIEAMAHGIEIIATLPDPIGVQRDLSTRPNGLAISKMRVPLGVVCMIYEARPNVTAD 130 Query: 422 IASLAIRSGNGLLLKGGKEAIRSNTILHKVITDAIPR-NVGEKLIGLVTTRDE--IADLL 478 +L +SGN ++L+GGKEA+ ++ ++ V+ + + + LI +V D + +L+ Sbjct: 131 AGALCFKSGNAVILRGGKEALHTSKVIASVLQKVLKQYGLPASLIAVVPDPDRALLMELM 190 Query: 479 KLDDVIDLVIPRGSNKLVSQIKASTKIPVLGHADGICHVYIDKSADMDMAKHIVMDAKID 538 + D ID++IPRG L++ + +K+PV+ H G+CH+Y+DK AD+D A ++++ K Sbjct: 191 QQRDTIDVIIPRGGEGLINFVTEHSKVPVIQHFKGVCHLYVDKDADLDKALALLLNGKTQ 250 Query: 539 YPAACNAMETLLVHKDLMKSPGLDDILVALKTEGVNIYGGPIAHKALGFPKAVS---FHH 595 CNA+E LLVH ++ L AL V I + + +S F Sbjct: 251 RTGVCNALEGLLVHSEVAPK-FLAMAATALAKHQVKINCCANTQQYFAAAQVLSDEEFGQ 309 Query: 596 EYSSMACTVEFVDDVQSAIDHIHRYGSAHTDCIVTTDDKVAETFLRRVDSAAVFHNASTR 655 EY + V V D A+ HIHR+GS HT+ I T ++ A+ F R VD++ V NAS+R Sbjct: 310 EYLDLELAVRQVKDFDQAVAHIHRFGSRHTEVICTENELTAKRFQRTVDASVVMVNASSR 369 Query: 656 FSDGARFGLGAEVGISTGRIHARGPVGVEGLLTTRWILRGRGQV 699 FSDG GLGAE+GI+T ++HA GP+G+E L T ++++ G GQ+ Sbjct: 370 FSDGGELGLGAEIGIATTKLHAYGPMGLESLTTEKYLVNGDGQI 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: 577 Number of extensions: 26 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: 415 Length adjustment: 35 Effective length of query: 681 Effective length of database: 380 Effective search space: 258780 Effective search space used: 258780 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