Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_028586043.1 G494_RS0120720 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_000429965.1:WP_028586043.1 Length = 473 Score = 217 bits (553), Expect = 7e-61 Identities = 148/484 (30%), Positives = 239/484 (49%), Gaps = 22/484 (4%) Query: 39 LVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERA 98 + ING +E + + NPA+ E ++ +V+ ++E A AI AAA AF W T+ ER+ Sbjct: 1 MFINGTWLERQDQFPVTNPANGE-LIAQVANGTREDAATAIAAAAAAFPAWSQTTSYERS 59 Query: 99 AVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVN 158 A+L+RA +R ++ E + L+ +E GKP A + A DF+ ++A + + + Sbjct: 60 ALLYRAHQLMREQQEELARLMTREQGKPLAAARIEVAYGADFLLWFAEEAKRIYGETIPS 119 Query: 159 SREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFV 218 +R ++ + P GV + PWN+ +++ + G TVVLKPA ATP+ A Sbjct: 120 ARSNQRFLVQHRPVGVVGAVTPWNYPVSMITRKVAPALAAGCTVVLKPAEATPLTAMALF 179 Query: 219 EVLEESGLPKGVVNFVPGS-GAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQ 277 + +G P G VN V + A +G+ +P +TFTGS VG ++ AA Sbjct: 180 RIFAAAGAPAGCVNLVTAAEPAPIGEEFCTNPLVRKLTFTGSTAVGKQLATLAA------ 233 Query: 278 QHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVL 337 LKRV E+GG +V DAD AA+ F GQ C +R VH + + + Sbjct: 234 PQLKRVSMELGGHAPFIVFADADPVHAAKGAALVKFLNTGQACICPNRIYVHRSILEPFV 293 Query: 338 ERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG-----TGD 391 + +++ + V +GP+++Q + DK+ + + G L+ GG G Sbjct: 294 QTLLDRITAMRAGNGLDQGVQVGPLVNQAALDKVDAQVRDAVDRGASLLCGGHRLTDRGL 353 Query: 392 DSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITN 451 D +G F PT+ + P+ + +EE FGPV A D D+ + +AN+T+YGL V T Sbjct: 354 D-QGTFYAPTLLTGVRPEMLIYREETFGPVAAVIPFDDRDDIIAMANDTDYGLAAYVYTR 412 Query: 452 NRKHIERAKQEFHVGNLYFNR-NCTGAIVGYHPFGGFKMSG---TDSKAGGPDYLALHMQ 507 + K R+ ++ G + N N T A PFGG K+SG ++ G +YL + + Sbjct: 413 DLKRALRSFEQLQFGMVGINDINPTSAAA---PFGGIKLSGLGREGARLGLEEYLDVRLA 469 Query: 508 AKTI 511 TI Sbjct: 470 GITI 473 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: 525 Number of extensions: 20 Number of successful extensions: 7 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: 473 Length adjustment: 34 Effective length of query: 481 Effective length of database: 439 Effective search space: 211159 Effective search space used: 211159 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