Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_011189829.1 DP_RS13140 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000025945.1:WP_011189829.1 Length = 418 Score = 266 bits (680), Expect = 2e-75 Identities = 144/409 (35%), Positives = 240/409 (58%), Gaps = 7/409 (1%) Query: 297 DMAVAARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMV 356 ++ V A+ ++ L +L++ + +L + + L A ++ ENE D+A+ +E GL ++M+ Sbjct: 9 EVGVRAKAAAADLMSLATRQKDAVLSQVGELLVAEKAFLQEENEKDLAAGREKGLSDAML 68 Query: 357 ARLVMTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRP 416 RL +T I S+ ++++ + DP+GR L + +GL + + PLGV+ +++ESRP Sbjct: 69 DRLALTDSVIESMVKGLKEVIALPDPVGRTLGSVKRPNGLSVGRMCVPLGVIAMIYESRP 128 Query: 417 DALVQIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREE 473 + + A+L +++GN ++L+GG EA SN L ++ A+ E V + ++ RE Sbjct: 129 NVTIDAAALCLKAGNAIILRGGSEAIHSNLALASILRRALEEAEVNPDSVQVIPMIDREA 188 Query: 474 IPDLLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVS 533 I +L L+D IDLVIPRG L+ + + IPVL H G+CH Y+DK D IV Sbjct: 189 ITIMLGLEDSIDLVIPRGGEGLIRFVSKNSSIPVLKHYKGVCHAYIDKDADLAKVAPIVI 248 Query: 534 DAKLDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRA---SKILNIPEA 590 +AK P CNA+E +L+H+D+ + VL L L GV + G ++ S+ + Sbjct: 249 NAKTQRPGVCNALEGILIHEDIVAD-VLPGLATELAELGVEMRGCSQSLPFSEHIVAASE 307 Query: 591 RSFNHEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFH 650 + E+ V+VV A +I ++GS HT+ I+TE++ A F+ +VD++AV Sbjct: 308 EDWGTEFLRLCLCVKVVRSFEDAKSYIRKYGSQHTEAIITENYTTAHRFVAEVDASAVVV 367 Query: 651 NASTRFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 NASTRF+DG GLGAE+G+ST ++HA GP+G+E L T ++++ G GQ+ Sbjct: 368 NASTRFNDGGELGLGAEIGISTTKLHAYGPMGLEELTTKKFVILGDGQI 416 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: 605 Number of extensions: 21 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: 418 Length adjustment: 36 Effective length of query: 681 Effective length of database: 382 Effective search space: 260142 Effective search space used: 260142 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