Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 151 bits (381), Expect = 6e-41 Identities = 153/472 (32%), Positives = 228/472 (48%), Gaps = 42/472 (8%) Query: 4 HYIAGQWLAG-QGETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQ 61 ++I G+W+A G+ ++ PV GQ R +DA ++ A+ AA A AW + + + Sbjct: 21 NFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPR-SDAQDIELALDAAHAAKDAWGKTSVTE 79 Query: 62 RIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNK-VAISVQAFRERTG-- 118 R +L R A ++ + LA ET WE+ V +N + + V FR G Sbjct: 80 RSNILLRIADRVEQNLEYLAVA---ET----WENGKAVRETLNADLPLFVDHFRYFAGCI 132 Query: 119 ---EKSGPLADATAVLRH--KPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSEL 173 E S D V H +P GVV P+NFP + I PAL AGNCVV KP+E Sbjct: 133 RAQEGSAADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQ 192 Query: 174 TPKVAELTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQ 232 TP V+ L L I+ LP GVLN+V G G E G ALA + + L FTGS+ G + + Sbjct: 193 TP-VSILVLLELIEDLLPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHI-LK 250 Query: 233 FGGQPQKILALEMGGNNP-LVVEEVAD-----LDAAVYTIIQSAFISAGQRCTCARRLLV 286 + +E+GG +P L +V D LD AV ++ AF + G+ CTC R+L+ Sbjct: 251 CAAESLIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGML-LAFFNQGEVCTCPSRVLI 309 Query: 287 PQGAWGDALLARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHL-IGK--GA 343 + + D + +++A + T++ G P V + ++ E K +L IGK GA Sbjct: 310 QESIY-DRFIEKVLARAQTIKQG----NPLDTATQVGAQASQEQFDKILSYLAIGKDEGA 364 Query: 344 QPLLAMTQ-PIDG----AALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREAN 398 Q LL + ++G ++P I+ EE FGP++ V + D A A+ AN Sbjct: 365 QVLLGGSLCQLEGEQSKGYYISPTIMKGHNKMRIFQEEIFGPVISVTTFKDEAEALAIAN 424 Query: 399 ATQYGLAAGLLSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASG 450 T+YGL AG+ + R ++ +AG V W + A FGG SG Sbjct: 425 DTEYGLGAGVWTRDMNRAQRMGRGIQAGRV-WINCYHAYPAHAAFGGYKKSG 475 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: 572 Number of extensions: 36 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 ( 7.3 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 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