Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate PP_4811 PP_4811 Gamma-glutamyl phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Putida:PP_4811 Length = 423 Score = 280 bits (716), Expect = 1e-79 Identities = 150/404 (37%), Positives = 241/404 (59%), Gaps = 6/404 (1%) Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360 AARE+SR + S+ + + L ADAL+A + A NELD+A+ + +GLE +++ RL Sbjct: 15 AAREASRVIGRASTAQKNRALQAAADALDAARAELTAANELDLAAGRASGLEPALLDRLA 74 Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420 +TP +I + +R++A + DP+G + + G+ + K +PLGV+ I++ESRP+ + Sbjct: 75 LTPARIDGMITGLRQVASLPDPVGAIRDMSYRPSGIQVGKMRTPLGVIGIIYESRPNVTI 134 Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDL 477 ASL ++SGN +L+GG EA SN + I + E + ++ +V T RE + L Sbjct: 135 DAASLCLKSGNATILRGGSEAIHSNRAIATCIQRGLAEAGLPAAVVQVVETTDREAVGAL 194 Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537 + + + +D+++PRG L+ +I ++PV+ H DGICH+YV + D D A + +AK Sbjct: 195 ISMPEFVDVIVPRGGRGLIERISRDARVPVIKHLDGICHIYVSQHADLDKAWNVAFNAKT 254 Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNH 595 C AMETLLV + + + L E+ GV L G R I++ A ++ Sbjct: 255 YRYGICGAMETLLVDQQVAER-FLPEMARRFVEKGVELRGCERTQAIISAKPATEADWHT 313 Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655 EY ++ VV+ + AI+HI+ +GS HTD I++E A F+ +VDSA+V N T Sbjct: 314 EYLDAILSIRVVDGLNQAIEHINHYGSHHTDSIISEHQGEARQFMAEVDSASVMLNTPTC 373 Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 F+DGF +GLGAE+G+ST ++HARGPVG+EGL ++++ G GQ+ Sbjct: 374 FADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYVVIGDGQL 417 Lambda K H 0.318 0.135 0.378 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: 602 Number of extensions: 15 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: 717 Length of database: 423 Length adjustment: 36 Effective length of query: 681 Effective length of database: 387 Effective search space: 263547 Effective search space used: 263547 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