Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate BWI76_RS05835 BWI76_RS05835 gamma-glutamyl-phosphate reductase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Koxy:BWI76_RS05835 Length = 417 Score = 288 bits (737), Expect = 4e-82 Identities = 159/405 (39%), Positives = 251/405 (61%), Gaps = 11/405 (2%) Query: 298 MAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVA 357 M +AA+ +S KL LSS ++ ++L IAD LEA I N D+A A+ GL E+++ Sbjct: 5 MGIAAKAASYKLAQLSSREKNQVLEKIADYLEAQTDAILRANAEDLAEARANGLSEALLD 64 Query: 358 RLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPD 417 RL + P ++S +A VR++ + DP+G+V+ + GL +E+ PLGV+ +++E+RP+ Sbjct: 65 RLALNPARLSGIANDVRQVCSLADPVGQVIDGGLLDSGLRIERRRVPLGVVGVIYEARPN 124 Query: 418 ALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLVTS--REEI 474 V +ASL +++GN +L+GGKE R+NA KVI A+ E + + + S R + Sbjct: 125 VTVDVASLCLKTGNAAILRGGKETWRTNAATVKVIQQALQECGLPAATVQAIESPDRALV 184 Query: 475 PDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSD 534 ++LK+D ID++IPRG L + + IPV+ G+CH+Y+D + D A +++ + Sbjct: 185 GEMLKMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYIDHSADVAEALKVIVN 244 Query: 535 AKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL-NIP----- 588 AK+ P+ACN++ETLLVH+D+ + L L + +GV+L+ + L N P Sbjct: 245 AKVQRPSACNSVETLLVHQDIAER-FLPALSKQMAESGVSLHADAASLPALQNGPASVEP 303 Query: 589 -EARSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAA 647 +A +++EY + V+VV D A+ HI HG+ H+D I+T A F+ +VDS+A Sbjct: 304 VKAEQYDNEYLSLDLNVKVVADQDEAVAHIREHGTQHSDAILTRTLGNANRFINEVDSSA 363 Query: 648 VFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWI 692 V+ NASTRF+DG +FGLGAEV VST ++HARGP+G+E L T +WI Sbjct: 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWI 408 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: 584 Number of extensions: 23 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: 417 Length adjustment: 35 Effective length of query: 682 Effective length of database: 382 Effective search space: 260524 Effective search space used: 260524 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