Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >NCBI__GCF_001046645.1:WP_066609128.1 Length = 487 Score = 208 bits (530), Expect = 3e-58 Identities = 154/457 (33%), Positives = 225/457 (49%), Gaps = 8/457 (1%) Query: 5 YIAGQWL-AGQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRI 63 +I G W+ A G T+ +P ++ + AA+ AA AFPAW + R Sbjct: 16 FIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAAFPAWKAQTAGDRA 75 Query: 64 ELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVA-ISVQAFRERTGEKSG 122 +LER+ A + + +L R++ E GKP+ E+ E+ + + + + R G Sbjct: 76 AVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFAEEGRRVDGGIVPA 135 Query: 123 PLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTL 182 P A+ ++ +P GV A P+NFP + PAL AG VV KPSELTP A Sbjct: 136 PEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVKPSELTPFTALALA 195 Query: 183 KAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKIL 241 K +AG+PAGV N+V G G AL A + L FTGS+R G+LL Q +++ Sbjct: 196 KLAEEAGIPAGVFNIVTGLPTAIGGALTASPVVRKLSFTGSTRVGSLLMRQCADTIKRV- 254 Query: 242 ALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVA 301 + E+GGN PL+V + AD+D AV + + S F +AGQ C CA R+LV G + D +L Sbjct: 255 SFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDGVY-DQFAEKLAR 313 Query: 302 VSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTP 361 + L+V D + +G +I+++A E + E + GA GA TP Sbjct: 314 AVSALKVAPGD-RTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAANDATGARFATP 372 Query: 362 GILDVSAVAER-PDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFL 420 IL + R EE FGP+ + R++ I ANAT YGLAA +++ R + Sbjct: 373 VILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYTENLHRAFRVA 432 Query: 421 VESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAY 457 AG+V N A APFGG+ SG R A+ Sbjct: 433 ERLEAGMVALNSGAI-AMEVAPFGGVKMSGLGREGAH 468 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: 552 Number of extensions: 29 Number of successful extensions: 7 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: 487 Length adjustment: 34 Effective length of query: 453 Effective length of database: 453 Effective search space: 205209 Effective search space used: 205209 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