Align δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized)
to candidate WP_090445196.1 BLS63_RS13480 glutamate-5-semialdehyde dehydrogenase
Query= metacyc::AT2G39800-MONOMER (717 letters) >NCBI__GCF_900100495.1:WP_090445196.1 Length = 422 Score = 278 bits (710), Expect = 5e-79 Identities = 151/404 (37%), Positives = 237/404 (58%), Gaps = 6/404 (1%) Query: 301 AARESSRKLQALSSEDRKKILLDIADALEANVTTIKAENELDVASAQEAGLEESMVARLV 360 AAR +SR + S+ + + LL A+AL+A + A N+ D+A+ + +GLE +++ RL Sbjct: 15 AARAASRVVARASTAQKNRALLAAAEALDAARAELAAANQQDLAAGRASGLEPALLDRLA 74 Query: 361 MTPGKISSLAASVRKLADMEDPIGRVLKKTEVADGLVLEKTSSPLGVLLIVFESRPDALV 420 +TP +I + +R++A + DP+G + + G+ + K PLGV+ I++ESRP+ + Sbjct: 75 LTPARIDGMIEGLRQVAGLSDPVGAIRDMSYRPSGIQVGKMRVPLGVIGIIYESRPNVTI 134 Query: 421 QIASLAIRSGNGLLLKGGKEARRSNAILHKVITDAIPET---VGGKLIGLVTSREEIPDL 477 ASL ++SGN +L+GG EA SN + I + + T R + L Sbjct: 135 DAASLCLKSGNATILRGGSEAIHSNRAIAACIQRGLAAAGLPAAAVQVVETTDRAAVGAL 194 Query: 478 LKLDDVIDLVIPRGSNKLVTQIKNTTKIPVLGHADGICHVYVDKACDTDMAKRIVSDAKL 537 + + + +D+++PRG L+ +I ++PV+ H DGICHVYVD D + A++I +AK Sbjct: 195 IAMPEFVDVIVPRGGKGLIERISRDARVPVIKHLDGICHVYVDALADLEKARQIAFNAKT 254 Query: 538 DYPAACNAMETLLVHKDLEQNAVLNELIFALQSNGVTLYGGPRASKILNIPEA--RSFNH 595 C AMETLLV + + A L + GV L G R ++ A ++ Sbjct: 255 YRYGICGAMETLLVDQAVAA-AFLPGMAQLFAEKGVELRGCERTRALIEAKPATEEDWST 313 Query: 596 EYCAKACTVEVVEDVYGAIDHIHRHGSAHTDCIVTEDHEVAELFLRQVDSAAVFHNASTR 655 EY A ++ VV+D+ AI+HI+R+GS HTD IVTE A FL +VDS++V NA T Sbjct: 314 EYLAPILSIRVVDDLEQAIEHINRYGSHHTDAIVTEHQGHARRFLAEVDSSSVMLNAPTC 373 Query: 656 FSDGFRFGLGAEVGVSTGRIHARGPVGVEGLLTTRWIMRGKGQV 699 F+DGF +GLGAE+G+ST ++HARGPVG+EGL ++++ G GQ+ Sbjct: 374 FADGFEYGLGAEIGISTDKLHARGPVGLEGLTCEKYVVIGDGQL 417 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: 591 Number of extensions: 22 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: 422 Length adjustment: 36 Effective length of query: 681 Effective length of database: 386 Effective search space: 262866 Effective search space used: 262866 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: 53 (25.0 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