Align Gamma-glutamyl phosphate reductase; GPR; EC 1.2.1.41; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase (uncharacterized)
to candidate Pf1N1B4_4438 Gamma-glutamyl phosphate reductase (EC 1.2.1.41)
Query= curated2:B0T315 (419 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4438 Length = 500 Score = 117 bits (292), Expect = 1e-30 Identities = 112/390 (28%), Positives = 179/390 (45%), Gaps = 48/390 (12%) Query: 47 ILAANAKDLEKAGAGGLTAPMVERLMLNPERLEDVAAGVEAVAAIPDPLGVETARWTRPN 106 I AAN D+E+A A G + RL+ + D+ AG+ A P G + + Sbjct: 100 IAAANLADIERAKARGRSTT---RLLADERMRGDMIAGLRAWRDAPATRG-KVVSCVEHD 155 Query: 107 GLDIARVRTPIGVIAMIFESRPNVTADAAALCVRSGNAVILRGGSECIHSNLAIHA-AIA 165 G + +V +P+G++A +FE RPNV ADAA + +R+GN +LR GS+ + + AI A+ Sbjct: 156 GWKVEQVVSPLGIVAFVFEGRPNVFADAAGV-LRTGNTAVLRIGSDALGTAQAIVTHALN 214 Query: 166 KGLKAAGISSDAVQIVRTPDRDAVGAILGGLNRTIDLIIPRGGKSLVAR---VQAEARVA 222 L AG+ + AV +V + + A A+ +R + L + RG V++ + +A A Sbjct: 215 PALADAGLPTGAVSLVESVNHAAGWAMFA--DRRLSLAVARGSGRAVSQLGSIAQQAGTA 272 Query: 223 VLGHLEGLNHVFVHAAADPRKAVEIVLNAKMRRVSVCGSAETLLVDRAAAERLLPPIADA 282 V H G + AD ++ +V N+ R+V C + L+ R A L+P DA Sbjct: 273 VSLHGTGGAWLIADKDADAQRFAAVVRNSLDRKV--CNTLNVCLIHRDRAAELVPLFLDA 330 Query: 283 LIKAGCELRGDGPSRAIEPTMKPAVEADWS-------------TEYLA------------ 317 L +AG RG G I + + ADW TE L Sbjct: 331 LQQAGTA-RGQGCKLHIVEGSEACLPADWQSASVEVYRAEGYQTEALTEPLPEDQLGREW 389 Query: 318 -----PVISVAVVDGVEGAAAHIAAYGSGHTDAIVTEDVAAAERFIALVDSAIVLVNAST 372 P +S+ +VD +E A Y T ++++ED A ERF V++ V N T Sbjct: 390 EWEETPEVSLKIVDDLEQAIVLFNRYSPQFTVSLISEDAQAQERFYNAVNAPFV-GNGIT 448 Query: 373 QFADGGEFGFGAEIGIA---TDKLHARGPV 399 ++ DG E+G++ + +L AR + Sbjct: 449 RWVDGQYALNKPELGLSNWESGRLFARSAI 478 Lambda K H 0.318 0.132 0.373 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: 358 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 419 Length of database: 500 Length adjustment: 33 Effective length of query: 386 Effective length of database: 467 Effective search space: 180262 Effective search space used: 180262 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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