Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_067910653.1 AQZ52_RS11395 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_001519075.1:WP_067910653.1 Length = 481 Score = 243 bits (621), Expect = 9e-69 Identities = 156/471 (33%), Positives = 241/471 (51%), Gaps = 22/471 (4%) Query: 35 KDYPLVINGE---RVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRY 91 K P ING+ + A ++NPA EEV RV+ + ++A+ AA AF+ + Sbjct: 5 KPLPSYINGQWALPATSTALFEAVNPAT-EEVCARVALCGPDDVDRAMAAARAAFDGYST 63 Query: 92 TSPEERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIEL 151 TS EER A++ + A R E + E G P++ + AE + ++ + Sbjct: 64 TSLEERLALVEKLIAVFEARYDEMVTAISTEMGAPYDLSYNAQAEC---GPGHLKETVRA 120 Query: 152 AKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATP 211 A+ + G + + V+ GV +I PWN+ +A +V G T+VLKP+ P Sbjct: 121 AREMVWERQLGSRGRLVHEAVGVCALITPWNWPINQLAAKIGPALVAGCTMVLKPSEIAP 180 Query: 212 VIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAA 271 + A F E + E+G P GV N V G+G +GD L HP+ +++FTGS G ++ + AA Sbjct: 181 LSAQLFAEFIHEAGFPAGVFNMVHGTGPGIGDALTGHPEADMVSFTGSTRAGIQVAKSAA 240 Query: 272 KVQPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEK 331 + +KRV E+GGK +V DA +E A F GQ C+A +R +V Sbjct: 241 ET------VKRVSQELGGKSPNLVFADAGLEAAVTRGVRHCFNNTGQSCNAPTRMLVEAS 294 Query: 332 VYDQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTG 390 VYD+ +E + ES P ++GPV+ + +++I IE G EG RLV+GG G Sbjct: 295 VYDEAVEIAKSVAESVQLGDPMEKGPHIGPVVSKVHFERIQKLIEAGIAEGARLVTGGPG 354 Query: 391 ---DDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGA 447 ++GY+++PTIFAD+ + + +EEIFGPV+ D +A+ +AN+T YGL Sbjct: 355 RADGFNRGYYVQPTIFADVTNQMTIAREEIFGPVLTMIPFKDEADAVAIANDTPYGLAAY 414 Query: 448 VITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGY-HPFGGFKMSGTDSKAG 497 V T + R ++ G++Y N GA Y PFGG+K SG + G Sbjct: 415 VQTGDLDRARRVARQLRAGSVYLN----GAGQEYCSPFGGYKQSGNGREWG 461 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: 599 Number of extensions: 32 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: 481 Length adjustment: 34 Effective length of query: 481 Effective length of database: 447 Effective search space: 215007 Effective search space used: 215007 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