Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_019557656.1 F612_RS0110120 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_000381085.1:WP_019557656.1 Length = 417 Score = 290 bits (743), Expect = 7e-83 Identities = 155/405 (38%), Positives = 247/405 (60%), Gaps = 10/405 (2%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 AR +SR L +++D+ + LL +ADAL+ + +KAEN D+ + ++ GL+ +M+ RL + Sbjct: 14 ARAASRALVRATTKDKNRALLAMADALQKSAELLKAENAKDLENGKKNGLDAAMLDRLAI 73 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 T I+ + ++++A ++DPIG + + + G+ + K PLGV+ I++ESRP+ + Sbjct: 74 TDAGIAGMIEGLQQVAALQDPIGEISEMSFRPSGIQIGKMRVPLGVVGIIYESRPNVTID 133 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAI-----PETVGGKLIGLVTSREEIPD 476 A+L ++SGN +L+GG EA SN L K I + PET + T RE + + Sbjct: 134 AAALCLKSGNAAILRGGSEATYSNQALAKCIQQGLAAVGLPETA--VQVVETTDREAVGE 191 Query: 477 LLKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAK 536 L+ + + +D++IPRG L+ +I ++PV+ H DGICHVY+D + D + A R+ +AK Sbjct: 192 LIAMPEFVDVIIPRGGKGLIERISQNARVPVIKHLDGICHVYIDDSADYNKAIRVAVNAK 251 Query: 537 LDYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKIL--NIPEARSFN 594 CNAMETLL+ + + VL EL GV L G + I+ N + Sbjct: 252 THRYGVCNAMETLLIAES-QAARVLPELAKQFGDKGVELRGCKKTCAIIKANAATEEDWA 310 Query: 595 HEYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNAST 654 EY A ++ VV+DV A+DHI ++ S HT+ I+TE+ ++ FL +VDS++V N ST Sbjct: 311 TEYLAPILSIRVVKDVDMAMDHIAKYSSGHTESIITENFTISRRFLAEVDSSSVMVNVST 370 Query: 655 RFSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 RF+DGF +GLGAE+G+ST + HARGPVG+EGL + ++I+ G G + Sbjct: 371 RFADGFEYGLGAEIGISTDKFHARGPVGLEGLTSQKYIVLGDGNI 415 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: 577 Number of extensions: 24 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: 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 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