Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_089303116.1 CHB84_RS19545 aldehyde dehydrogenase
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_900188115.1:WP_089303116.1 Length = 503 Score = 249 bits (637), Expect = 1e-70 Identities = 160/462 (34%), Positives = 234/462 (50%), Gaps = 22/462 (4%) Query: 62 QVIGVVSKASREIVDDAFKSAETAFH--TWKNVNPEERANILIRAAAIIRRRKHEFSAWL 119 +VIG ++AS VD A +A +F TW ER +L R ++R E Sbjct: 43 EVIGEFARASATDVDAAVAAARRSFEAGTWSRARAGERIAVLQRYGRLLREHADELRGLQ 102 Query: 120 VKEAGKPWKEAD---ADTAEAIDFLEYYARQMITLKDGKPVNSREGEH-NRYFYTPIGVC 175 + P A D +++A + + + G+H F P+GV Sbjct: 103 ALDNSVPLSFGSIYATSVGAAADVFDHHAGWVDKIGGQTLPPYQGGDHLTMTFREPLGVV 162 Query: 176 VTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLPKGVVNFVP 235 I PWN + A + G +V+LKP+ + VE+L EAGLP GV+N V Sbjct: 163 AAILPWNAPFLLFAQKVAPALAAGCSVVLKPSEYATYSVLRMVELLAEAGLPAGVLNMVT 222 Query: 236 GSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEMGGKDTVVV 295 G+G + G+ LI H ++FTGSR VG R+ E +A LKRV +E+GGK VV Sbjct: 223 GTGEECGEALITHSDVDKVSFTGSRGVGKRIVEASAGT------LKRVSLELGGKSPAVV 276 Query: 296 DKDA-DLDLAAQSIVTS-AFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQLSVGEPT 353 DA D+ +AA ++V + G SGQ C A +RA++H+D+YD LE A + ++ G+P Sbjct: 277 FDDAPDVTIAASTVVGAVTMGLSGQACVANTRALVHRDIYDEFLEAAKGMASAITFGDPF 336 Query: 354 APDVYMGPVVDQGAFSKIMSYIEVGKEEGRLMVGG----EGDDSKGFFIQPTIFADVDPH 409 P V P++++ +++ YI GKEEG +V G EG+ S G F+ PTIFADVD Sbjct: 337 DPGVLASPLINEQQLERVLGYIAKGKEEGATLVMGGERLEGEYSAGNFVSPTIFADVDNS 396 Query: 410 ARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRDFHVGNLY 469 + I QEEIFGPV++ D + A+ +AN+TEYGL V T++ + R G + Sbjct: 397 STIAQEEIFGPVLSVVPFGDEEEAIRLANDTEYGLGAGVFTSDVQRAFRVSRGVRAGTVG 456 Query: 470 FNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTV 511 N + + PFGGFK SG + GG + + KTV Sbjct: 457 IN---GFQLEPHAPFGGFKQSGL-GREGGQSAFEAYTELKTV 494 Lambda K H 0.318 0.135 0.394 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: 627 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: 503 Length adjustment: 34 Effective length of query: 481 Effective length of database: 469 Effective search space: 225589 Effective search space used: 225589 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 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