Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_003471449.1 J416_RS11040 aldehyde dehydrogenase family protein
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_000359605.1:WP_003471449.1 Length = 473 Score = 262 bits (670), Expect = 2e-74 Identities = 162/470 (34%), Positives = 252/470 (53%), Gaps = 21/470 (4%) Query: 37 YPLVINGERVTTDDKIVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEE 96 Y L ING V T++ I V + V+KASRE VD+A SA A+ ++P + Sbjct: 4 YALYINGGWVETEETI-DVLDKYSQTTYATVAKASREHVDEAISSATKAYRK-NQLSPYQ 61 Query: 97 RANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLK-DGK 155 R IL + +++ K E + + KEAGKP K+A + + + A + + +G Sbjct: 62 RFEILRNVSTLMKNNKEELAYTITKEAGKPLKQARTEIDRSAETFLLAAEEAKRIHGEGV 121 Query: 156 PVNSREGEHNRYFYT---PIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPV 212 PV + G +R +T P+GV ISP+NF L ++A + GN V+LKPAS TP+ Sbjct: 122 PVEAAPGSEHRMAFTIKVPVGVVGAISPFNFPLNLVAHKVAPALAAGNAVVLKPASKTPL 181 Query: 213 VAAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAV 272 + K ++LEEAGLPKG++ V GSG+ +G ++D + L TFTGS +VG++L + Sbjct: 182 ASLKLAKLLEEAGLPKGLLQVVVGSGSVVGQQMMDDERIDLYTFTGSAEVGLQLKQNTG- 240 Query: 273 VHPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDV 332 L R+I+E+G V+VDK+AD+D AA+++ +F F+GQ C + R +H+ + Sbjct: 241 -------LNRLILELGNNSPVIVDKEADIDHAAKTLAGQSFAFAGQVCISVQRVYVHESI 293 Query: 333 YDVVLEKAVALTKQLSVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGGEGD 391 + LE KQL VG+PT +GP++ + ++I ++G ++++GG+ Sbjct: 294 QERFLETFSEQIKQLLVGDPTDATTDVGPMISVSEAERAETWIHEAVDKGAKVVLGGK-- 351 Query: 392 DSKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITT 451 +G ++PTI DV P R++ EEIF PVV+ D D +E N + YGL G + T Sbjct: 352 -REGALLEPTILTDVKPEMRVVCEEIFAPVVSVIAYTDLDSCIEEVNQSVYGLQGGIFTQ 410 Query: 452 NRHHIEKAKRDFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDY 501 N A + VG N + + V P+GG K SG + GP Y Sbjct: 411 NIDTAYYAAKRVEVGGFMIN-DGSQYRVDLMPYGGVKDSGNGKE--GPKY 457 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: 558 Number of extensions: 21 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: 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 (21.7 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