Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate Synpcc7942_2265 Synpcc7942_2265 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__SynE:Synpcc7942_2265 Length = 431 Score = 339 bits (869), Expect = 2e-97 Identities = 188/420 (44%), Positives = 262/420 (62%), Gaps = 7/420 (1%) Query: 299 AVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVAR 358 A A R ++R+L S DR+++L IA LE I A N+ D +A G+ ++ AR Sbjct: 12 AQATRAAARQLAQWSGADRQRLLSAIATTLEQEAPRILAANQADCEAATTEGIAPALYAR 71 Query: 359 LVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDA 418 L + K+++ A VR LA + DP+G++ E+ +GL+L++ + P+GVL ++FE+RPDA Sbjct: 72 LKLDADKLAAAIAGVRDLAQLPDPLGQIQIDRELDEGLILQRLTCPVGVLGVIFEARPDA 131 Query: 419 LVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPETVGG-KLIGLVTSREEIPDL 477 ++QIASLAI+SGNG +LKGG+EA S + I A+ E + I L+TSREE L Sbjct: 132 VIQIASLAIKSGNGAILKGGREAICSCQAIVAAIAQALAEQQAPVEAIRLLTSREETLAL 191 Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537 LKLD +DL+IPRGSN V +++ T IPVLGHADGICH+YVD+A + I DAK Sbjct: 192 LKLDRYVDLIIPRGSNSFVRFVQDNTHIPVLGHADGICHLYVDQAAAIEKTVTITVDAKT 251 Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNH 595 YPAACNA+ETLL+H+ + L + AL GV+L G A I+ + A + Sbjct: 252 QYPAACNAIETLLIHEAIAPQ-FLPVVAAALHEKGVSLRGDAAAQTIVPMEAATEEDWRT 310 Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655 EY V +V + AI HI+ +GS HTD I TED A F QVDSA V+HN STR Sbjct: 311 EYSDLVLAVRLVPSLDAAIAHINEYGSGHTDAIATEDAAAAAQFFSQVDSAGVYHNCSTR 370 Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQVV---DGDNGIVYTHQD 712 F+DGFR+G GAEVG+ST ++ RGPVG+EGL+T ++++ G GQ+ G + H+D Sbjct: 371 FADGFRYGFGAEVGISTQKLPPRGPVGLEGLVTYKYVLSGDGQIAATYSGAQAKPFLHRD 430 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: 593 Number of extensions: 20 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: 431 Length adjustment: 36 Effective length of query: 681 Effective length of database: 395 Effective search space: 268995 Effective search space used: 268995 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