Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 203 bits (517), Expect = 1e-56 Identities = 158/465 (33%), Positives = 227/465 (48%), Gaps = 17/465 (3%) Query: 5 YIAGQWLAG-QGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRI 63 YIAG+ G G T +DP V + A VDAAV AAREAFP WA R Sbjct: 24 YIAGRLTKGTSGRTHAVVDPATGEEVHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRS 83 Query: 64 ELLERFAATLKSRADELARVIGEETGKPLWESAT-EVTSMVNKVAISVQAFRERTGEKSG 122 + L RFA L RA++ AR + GKPL + +V ++ A A R G+ +G Sbjct: 84 DALHRFAEVLADRAEDFARAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHLQGQSAG 143 Query: 123 PLA-DATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELT 181 + D T+ +R +P GVV P+N+P + ++PA+ AGN +V KP+ELTP + L Sbjct: 144 EYSGDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLF 203 Query: 182 LKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKI 240 +A +AG+P GV+N+V G G+E G L H + + FTGS+ G + ++ K Sbjct: 204 AQAATEAGIPDGVINIVTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRV-AEIATASVKR 262 Query: 241 LALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLV 300 L LE+GG P VV + ADL+AAV + A I+ GQ CT A R V + + + +AR Sbjct: 263 LHLELGGKAPFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLY-EEFVARTA 321 Query: 301 AVSATLRVGRFDEQPAPFMGAVIS------LSAAEHLLKAQEHLIGKGAQPLLAMTQPID 354 A+ T+R+G P +G +IS ++ +A ++ G P + + Sbjct: 322 ALMETVRLGD-PFAPGTDLGPLISHVHRDRVAGFVDRARAYARVVTGGEAP---QGELKN 377 Query: 355 GAALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRE 414 GA I + +E E FGP+L V+ + IR AN T YGLAA S Sbjct: 378 GAYYRPTLIAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVY 437 Query: 415 RFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYA 459 R + E +AG V W S P GG SG + + Y+ Sbjct: 438 RANRATREIKAGCV-WVNDHIPIISEMPHGGSKQSGFGKDMSSYS 481 Lambda K H 0.318 0.134 0.396 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: 655 Number of extensions: 37 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: 487 Length of database: 511 Length adjustment: 34 Effective length of query: 453 Effective length of database: 477 Effective search space: 216081 Effective search space used: 216081 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