Align Gamma-glutamyl phosphate reductase 2; GPR 2; EC 1.2.1.41; Glutamate-5-semialdehyde dehydrogenase 2; Glutamyl-gamma-semialdehyde dehydrogenase 2; GSA dehydrogenase 2 (uncharacterized)
to candidate Synpcc7942_2243 Synpcc7942_2243 Glutamate-5-semialdehyde dehydrogenase
Query= curated2:Q55167 (420 letters) >FitnessBrowser__SynE:Synpcc7942_2243 Length = 414 Score = 377 bits (968), Expect = e-109 Identities = 190/386 (49%), Positives = 266/386 (68%), Gaps = 2/386 (0%) Query: 32 RSRAVLAMAEALERSFAQILEANTLDLVVSREMSVADCLCEWLKLTPERLQNTVTILKRL 91 RS+A+ A+A+A++ + ILEANTLDL ++ + D L WLKLTPERL TV IL+RL Sbjct: 27 RSQALQAIAQAIDSARDDILEANTLDLEACQDSEMPDLLRRWLKLTPERLDRTVEILERL 86 Query: 92 ASLPDPLQRVMASPYQFNLAQTYCQLMPLGVVALVYESFPELAAIAAGFCLKTGNSLVLR 151 + DP+Q+VM + +Q +Q Y QLMPLGV+A VYE+ PELAAIA G CL+ GNS++L+ Sbjct: 87 SVRSDPIQQVMRASFQHEHSQAYSQLMPLGVIAFVYEALPELAAIATGLCLRVGNSILLK 146 Query: 152 SCGASSHSTAAICEILREGLLDADLPVDSVSHIP-SETSPNVQDLVGNASQLNLVIPYGR 210 + H+ AI +++E L +LP S+ +P + + ++ LV ++LVIPYGR Sbjct: 147 GGTEAVHTNQAIVSVMQEALESTELPTTSLILLPEDDPATSLAALVTQDQWIDLVIPYGR 206 Query: 211 PSFVEQISQQCTPPVLKAAMGNCYLYWSSKGDLEMVRQMIIDSHVGHPDPVNAIEKVLVS 270 P V+Q+++ T PVL+ +MGNCYLYW+S G+LE VR MI+DSH PD VNAIEKVL+ Sbjct: 207 PELVQQVARLATSPVLRTSMGNCYLYWASGGELETVRWMILDSHASEPDAVNAIEKVLID 266 Query: 271 PGQNPAPLVRLLNNLQAKGFKLRGDAELCEQFPDHLTLAKENEWGKAYLDRTVAFRTTQN 330 N + L L+++L++KGF+L+GD EL ++ P+ L LA+ +W + YL RTVAF+ Sbjct: 267 RDCNLSKLTVLMDSLRSKGFRLKGDEELVQEMPE-LELARHEDWSRPYLSRTVAFKLVPG 325 Query: 331 LKTAIAWINSHSSGHGDCIATDSYQESRQFSMGVDSALVYVNIPPYFCRNPRHGESLFLG 390 ++ A WIN+HSSGH D I TDSY++SR FS ++SA+V+VN P F R+PRH + LG Sbjct: 326 IEAATDWINTHSSGHADSIVTDSYEDSRAFSRELNSAMVHVNASPRFSRSPRHSNEIALG 385 Query: 391 VSSQKGQRRGLIGLEAFMTPKQIVQG 416 +S+QKG RRG I LE T KQ+V G Sbjct: 386 MSNQKGYRRGRITLETLTTIKQVVLG 411 Lambda K H 0.319 0.133 0.394 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: 468 Number of extensions: 17 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: 420 Length of database: 414 Length adjustment: 31 Effective length of query: 389 Effective length of database: 383 Effective search space: 148987 Effective search space used: 148987 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: 50 (23.9 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