Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_041365250.1 METME_RS08100 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000214665.1:WP_041365250.1 Length = 418 Score = 277 bits (708), Expect = 9e-79 Identities = 152/404 (37%), Positives = 242/404 (59%), Gaps = 7/404 (1%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 AR + R++ S + LL IAD + A + EN D+ + +E GL+ + + RL + Sbjct: 14 ARLAGREISKSDSGRKNLALLKIADVIAAGSVELTGENRKDLQAGKENGLDAASLDRLEL 73 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 TP +I+++ ++++A + DP+G + + G+ + + PLGV+ I++ESRP+ V Sbjct: 74 TPARIAAMVEGLKQVAALPDPVGEITDLSFRPSGIQVGQMRVPLGVIGIIYESRPNVTVD 133 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDLL 478 A+L +++GN +L+GG E+ SN + IT + E + + + +V T R + +L+ Sbjct: 134 AAALCLKAGNACILRGGSESIHSNRAIAACITQGLLEAGLPQQAVQVVETTDRAAVGELI 193 Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538 L D +D+++PRG L+ +I + IPV+ H DGICHVY+D D D A I +AK Sbjct: 194 TLKDYVDVIVPRGGKSLIERISSEATIPVIKHLDGICHVYIDGKADLDKAVAIAMNAKTH 253 Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRA-SKILNIPEARS--FNH 595 CNAMETLLV + + VL L GV L G + S + N A ++ Sbjct: 254 RYGVCNAMETLLVAESVA-GTVLRILAAQYAEKGVELRGCLKTCSLVKNAVRATEDDWHT 312 Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655 EY A ++++V + AI HI+++ SAHT+ IVTED+ +A FLR+VDS++V NASTR Sbjct: 313 EYLAPILSIKIVAGIDEAITHINKYSSAHTESIVTEDYTLARRFLREVDSSSVMVNASTR 372 Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 F+DGF +GLGAE+G+ST ++HARGPVG+ GL + ++I+ G G + Sbjct: 373 FADGFEYGLGAEIGISTDKLHARGPVGLNGLTSLKYIVLGDGHI 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: 573 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: 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 10 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