Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_093395059.1 BM091_RS08720 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_900114975.1:WP_093395059.1 Length = 417 Score = 284 bits (726), Expect = 7e-81 Identities = 154/403 (38%), Positives = 245/403 (60%), Gaps = 6/403 (1%) Query: 302 ARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLVM 361 A+ +S + +++ + L IA+ L I+ N DV A+E+G+ + + RL++ Sbjct: 14 AKRASYLMAKATTDQKNNALAAIAEGLRRERGRIEEANRKDVEQARESGISGAKLDRLIL 73 Query: 362 TPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALVQ 421 + +S + A + ++ DP+G++ + +GL + + PLGV+ I++ESRP+ V Sbjct: 74 SEKVMSEMVAGIEEVIAWPDPVGKITGLWKRPNGLKVGRMRIPLGVIGIIYESRPNVTVD 133 Query: 422 IASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET-VGGKLIGLV--TSREEIPDLL 478 + L I+SGN ++L+GG EA SN L ++ + + + + + LV T RE + ++L Sbjct: 134 ASILCIKSGNAVVLRGGSEAFYSNQCLVGIMREGLRKAELPEDAVQLVPTTEREAVLEML 193 Query: 479 KLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKLD 538 KL++ +D++IPRG +L+ + ++PVL H G+CHVYVDK D MA+ + +AK+ Sbjct: 194 KLEEYVDVMIPRGGEELIRFVSENARMPVLKHYKGVCHVYVDKFADLSMAETVCVNAKVQ 253 Query: 539 YPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNHE 596 P CNAMETLLVH+DL L + S+GV L G PR +I+ EA + E Sbjct: 254 RPGVCNAMETLLVHRDLA-GKFLPRMKEVFDSHGVELRGCPRTREIIPCREATEEDWKAE 312 Query: 597 YCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTRF 656 Y V+VV+ + AIDHIH +GSAHT+ I+TE++E A F+ V S+ V NASTRF Sbjct: 313 YLDLILAVKVVDSMNEAIDHIHTYGSAHTEAIITENYERAWAFIESVQSSLVLVNASTRF 372 Query: 657 SDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 +DG++ GLGAE+G+ST ++HA GP+GV+ L TT++I G GQ+ Sbjct: 373 NDGYQLGLGAEIGISTSKLHAFGPMGVDELTTTKFIAFGNGQI 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: 599 Number of extensions: 29 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 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