Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_110207251.1 DNK54_RS12190 aldehyde dehydrogenase family protein
Query= SwissProt::P94391 (515 letters) >NCBI__GCF_003194585.1:WP_110207251.1 Length = 474 Score = 252 bits (643), Expect = 2e-71 Identities = 165/459 (35%), Positives = 232/459 (50%), Gaps = 10/459 (2%) Query: 41 INGE-RVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAA 99 + GE R T + I S NPA EVV A+ + +A+ AA KA + WR T ERAA Sbjct: 9 VGGEWRAGTGSAIESRNPARPHEVVASGHAATPDDVTEAVAAATKAAQAWRRTLMHERAA 68 Query: 100 VLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNS 159 VL R A + R L E GK E + A + + A Q + Sbjct: 69 VLRRTAELLEERADALGLELTLEEGKTLVEGIGEVRRAAEIFRFNAGQADREVGEVFASP 128 Query: 160 REGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVE 219 R GE+ P GV VI PWNF AI A ++ GN VV KPAS P++A + E Sbjct: 129 RRGERIVVTRKPIGVVAVITPWNFPIAIPAWKIAPALIHGNAVVWKPASIVPLLAVRLAE 188 Query: 220 VLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQH 279 L ++GLP GV++ + G GA +G + P +TFTGS +GT + + A ++ Sbjct: 189 ALHDAGLPAGVLSLIIGPGA-LGSQIASAPGVHAVTFTGSTGIGTGLLQLCAPLR----- 242 Query: 280 LKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLER 339 + V AEMGGK+ VV DAD+ELAA I A GQKC+A SR VV + V + + Sbjct: 243 -RPVQAEMGGKNAAVVFADADLELAADQIVLGAMRSTGQKCTATSRLVVEDSVAEDLRTL 301 Query: 340 VIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEGRLVSGGTGDDSKGYFIK 399 +++ E+ V +DV +GPV G+ +I S I+ + G V G+++ Sbjct: 302 LVQRIEALVVGDGTRSDVTVGPVSSGGAQAEITSMIDDALRGGARVVAQAEAPDDGHYVP 361 Query: 400 PTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIERA 459 PTI ++D + + +EE+FGPV+A +D D LE+AN +E+GL+ AV T++ R Sbjct: 362 PTIL-EVDVRQPIWREEVFGPVLAMTTGADEDRVLELANASEFGLSAAVFTSDLSRTLRI 420 Query: 460 KQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGG 498 E VG L+ N GA + PFGG K SG K G Sbjct: 421 MDELEVGVLHVNSESAGA-DPHVPFGGVKDSGIGPKEQG 458 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: 587 Number of extensions: 31 Number of successful extensions: 6 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: 474 Length adjustment: 34 Effective length of query: 481 Effective length of database: 440 Effective search space: 211640 Effective search space used: 211640 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