Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein
Query= curated2:Q2SXN9 (487 letters) >NCBI__GCF_000021485.1:WP_012536996.1 Length = 506 Score = 160 bits (404), Expect = 1e-43 Identities = 145/477 (30%), Positives = 224/477 (46%), Gaps = 30/477 (6%) Query: 5 FIDGAWVDGA-GPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARC 63 FI G WV G F + +P + + +SA+D+E A+ +A A AW + AR Sbjct: 22 FIGGRWVAPVRGEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAAKDAWGRTSVTARS 81 Query: 64 TIVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAP 123 I+ + A + E LA + GK + E ++ A V +S + G RA Sbjct: 82 NILLKIADRIDANLEMLAVAETWDNGKAVRE------TLNADVPLSSDHFRYFAGCLRAQ 135 Query: 124 MA-------DGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPG 176 + VA H P GVV P+NFP + + PAL AGN VV KP+E P Sbjct: 136 EGTIGEIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPA 195 Query: 177 VARATVEIWRDAGLPAGVLNLVQGEK-DTGVALANHRQIDGLFFTGSSDTGTLLHKQFGG 235 +E+ D LPAGVLN+V G + G ALA ++I + FTGS+ G+L+ K + Sbjct: 196 SILVMMELIADL-LPAGVLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMK-YAA 253 Query: 236 RPEIVLALEMGGNNP-LVVAEVEDI-DAAVHHAIQSA---FLSAGQRCTCARRILVPRGA 290 I +E+GG +P + A+V D DA V A++ A F + G+ CTC R+L+ Sbjct: 254 ENIIPSTVELGGKSPNIFFADVLDQEDAFVSKAVEGAVLAFFNQGEVCTCPSRLLIQESI 313 Query: 291 FGDRFVARLADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPI---- 346 + ++F+ + + +++I D + +GA S ++++ GA I Sbjct: 314 Y-EKFIGMVVERSAQIKRGN-PLDTEVMVGAQASQEQYDKILSYIQIGKDEGAEVITGGA 371 Query: 347 IEMKQRDPALGF-VNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLS 405 +E D G+ + +L TN + EE FGP+ + + D +A+A AND FGL Sbjct: 372 VETMSADYCEGYYIQPTLLKGTNNMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLG 431 Query: 406 AGLLADDEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAADY 462 AG+ D + R I+AG V W + + A FGG +SG R + D+ Sbjct: 432 AGVWTRDMNRAYRMGRGIQAGRV-WTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDH 487 Lambda K H 0.320 0.134 0.402 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: 476 Number of extensions: 23 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: 487 Length of database: 506 Length adjustment: 34 Effective length of query: 453 Effective length of database: 472 Effective search space: 213816 Effective search space used: 213816 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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