Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 186 bits (471), Expect = 2e-51 Identities = 152/465 (32%), Positives = 229/465 (49%), Gaps = 33/465 (7%) Query: 4 HYIAGQWLAGQGETLES-LDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQR 62 HYI G+W+ +G T ++P + V D AV AA+ AF +++R +++R Sbjct: 7 HYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDER 66 Query: 63 IELLERFAATLKSRADELARVIGEETGKPLWESAT-EVTSMVNKVAISVQAFRERTGEKS 121 I LLE A K+RA +LA I E G P+ + T +V S + + ++ A + E S Sbjct: 67 IALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALK--AFEFS 124 Query: 122 GPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELT 181 + + V H+P GVVA+ P+N+P + + PAL AGN +V KPSE P A + Sbjct: 125 EQIGQSLVV--HEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAAIF 182 Query: 182 LKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKI 240 + +AG+PAGV NLVQG G G AL+ HR +D + FTGS+R G + ++ + K Sbjct: 183 AEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAG-IQVAKNAAETVKR 241 Query: 241 LALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDAL----- 295 + E+GG +P V+ ADL AV + S +++GQ C R+LV + +A Sbjct: 242 VHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIASG 301 Query: 296 LARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDG 355 L + V + GR +G V++ + E + + +GA+ DG Sbjct: 302 LMKAVETGDPAQEGRH-------IGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDG 354 Query: 356 AAL-------LTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGL 408 L G+ + +A EE FGP++ +I Y D A+R AN T YGL+A + Sbjct: 355 IETGYFVKPTLFSGVRNDMTIAR---EEIFGPVITIIPYRDEEEAVRIANDTDYGLSA-V 410 Query: 409 LSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHR 453 L S E ++ RAG+V N S PFGG SGN R Sbjct: 411 LFGSPEEVKRVAPRLRAGMVYINGGQPD--PSLPFGGYKQSGNGR 453 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: 558 Number of extensions: 37 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 487 Length of database: 474 Length adjustment: 34 Effective length of query: 453 Effective length of database: 440 Effective search space: 199320 Effective search space used: 199320 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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