Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate 353244 BT3718 gamma-glutamyl phosphate reductase (NCBI ptt file)
Query= metacyc::AT2G39800-MONOMER (717 letters) >FitnessBrowser__Btheta:353244 Length = 417 Score = 254 bits (648), Expect = 8e-72 Identities = 146/417 (35%), Positives = 237/417 (56%), Gaps = 16/417 (3%) Query: 293 SNARDMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLE 352 +N A + +SR+L LS + +IL +ADA A + I +ENE D+A ++ + Sbjct: 3 TNLNGTFAAVQAASRELALLSDDTINQILNAVADATIAETSFILSENEKDLARMDKSNPK 62 Query: 353 ESMVARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVF 412 RL +T ++ +AA R +A + P+GR+LK+T +G+ L K S P GV+ I++ Sbjct: 63 YD---RLKLTEERLKGIAADTRNVATLPSPLGRILKETSRPNGMKLTKVSVPFGVIGIIY 119 Query: 413 ESRPDALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLVTS- 470 E+RP+ + SL ++SGN +LKGG +A SN + VI + + V ++ L+ + Sbjct: 120 EARPNVSFDVFSLCLKSGNACILKGGSDADDSNRAIISVIHKVLEKFHVNPHIVELLPAD 179 Query: 471 REEIPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKR 530 RE LL +DL+IPRGS+ L+ ++ +IPV+ GICH Y D+ DT Sbjct: 180 REATAALLNATGYVDLIIPRGSSNLINFVRENARIPVIETGAGICHTYFDEFGDTRKGAD 239 Query: 531 IVSDAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRA--------- 581 I+ +AK + CNA++ ++H+ ++ L L L+ + VT+Y +A Sbjct: 240 IIHNAKTRRVSVCNALDCTIIHE--KRLGDLPALCDQLKESKVTIYADTQAYQALEGYYP 297 Query: 582 SKILNIPEARSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLR 641 +++L SF E+ V+ V+ A+ HI + S H++CIVTE+ E A LF + Sbjct: 298 AELLQPATPESFGTEFLDYKMAVKTVKSFEDALGHIQENSSRHSECIVTENKERATLFTK 357 Query: 642 QVDSAAVFHNASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQ 698 VD+A V+ N ST F+DG +FGLGAE+G+ST ++HARGP+G+E + + +W++ G GQ Sbjct: 358 IVDAACVYTNVSTAFTDGAQFGLGAEIGISTQKLHARGPMGLEEITSYKWVIEGDGQ 414 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: 597 Number of extensions: 23 Number of successful extensions: 4 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