Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_043765410.1 U743_RS02990 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000733765.1:WP_043765410.1 Length = 508 Score = 245 bits (626), Expect = 2e-69 Identities = 163/480 (33%), Positives = 241/480 (50%), Gaps = 34/480 (7%) Query: 27 ATVSEYLGKDYPLVINGERVETEA--KIVSINPADKEEVVGRVSKASQEHAEQAIQAAAK 84 A ++Y K+Y I+G+ V+ + +I INPA+ + V+ + + E A +A+ AAA+ Sbjct: 14 AQAAKYFQKEYGHFIDGKWVQGASGERIPMINPANGQ-VLSHIQSGNAEDARRAVDAAAQ 72 Query: 85 AFEEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEA-DADTAEAIDFMEY 143 AF W T ER VL+ A ++R R +++ + + GKP EA D AI+ E Sbjct: 73 AFPAWSQTPRSERQRVLYEMARRLRARMADYAMMDCLDNGKPAMEAMHFDLPMAIEQFEI 132 Query: 144 YAR-------QMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPI 196 ++ Q I+ + RE P GV I PWN +MA + Sbjct: 133 FSGAPWFLHGQSIDAPNTLGIVLRE---------PLGVVAQIIPWNVPLIMMAAKLAPAL 183 Query: 197 VTGNTVVLKPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITF 256 GNTVVLKP+ + +F + + LP GVVN V G G VG+ LV HPK + F Sbjct: 184 AAGNTVVLKPSEIVCLSVLEFFREMADL-LPPGVVNVVTGYGPSVGEALVTHPKVRKVAF 242 Query: 257 TGSREVGTRIFERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFA 316 TGSR ++ + A+ ++ E+GGK +V EDAD++ AA+ S Sbjct: 243 TGSRPTAQKLMQYASV------NIIPQTMELGGKSANIVCEDADLDAAAEGAAMSTVLNK 296 Query: 317 GQKCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIE 376 G+ C AGSR VHEKV D L++ + + P +GP + + YDKIM Y+E Sbjct: 297 GEVCLAGSRVFVHEKVKDVFLDKFTSLLKRVKAGDPREPTTQIGPQVSKAQYDKIMGYLE 356 Query: 377 IGKQEG-RLVSGGTGDDSKGY----FIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFD 431 +G+QEG +L +GG G+ FI+PT+F D+D R+ QEEIFGPV D D Sbjct: 357 LGQQEGAKLAAGGRKAAPAGFEDGLFIEPTVFFDVDNSMRIAQEEIFGPVSCVIGFRDDD 416 Query: 432 EALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSG 491 E + +AN++ YGL G + T + R + G ++ NR +G P GG+K SG Sbjct: 417 EVVRMANDSVYGLGGGLWTKDLSRAHRIARALETGTVWVNRYYN--FLGGMPIGGYKQSG 474 Lambda K H 0.316 0.133 0.379 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: 602 Number of extensions: 30 Number of successful extensions: 5 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: 515 Length of database: 508 Length adjustment: 35 Effective length of query: 480 Effective length of database: 473 Effective search space: 227040 Effective search space used: 227040 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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