Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= SwissProt::O50174 (487 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 170 bits (430), Expect = 1e-46 Identities = 148/469 (31%), Positives = 224/469 (47%), Gaps = 26/469 (5%) Query: 4 HYIAGQWLAGQG-ETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQ 61 ++I GQW+A G E +++ P+ G + RG A V+ A+ AA +A AW + P + Sbjct: 21 NFIGGQWVAPLGGEYFDNISPITGHPICQVARGR-AADVELALDAAHKAKDAWGKTPAAE 79 Query: 62 RIELLERFAATLKSRADELARVIGEETGKPLWES-ATEVTSMVNKVAISVQAFRERTGEK 120 R +L + A L LA V + GKP+ E+ A ++ ++ R + G Sbjct: 80 RANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAGCLRAQEGSL 139 Query: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAEL 180 S D A H+P GVV P+NFP + + PAL AGNCVV KP+E TP ++ L Sbjct: 140 SEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTP-MSIL 198 Query: 181 TLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQK 239 + I LP GVLN+V G G E G LA+++ + + FTG + TG L+ Q+ + Sbjct: 199 AVAELIADLLPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLI-MQYAAENLI 257 Query: 240 ILALEMGGNNP------LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGD 293 + LE+GG +P ++ E+ A LD A+ A ++ G+ CTC R LV + + D Sbjct: 258 PVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFA-LNQGEVCTCPSRALVQRSIY-D 315 Query: 294 ALLARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPI 353 + + +A A +R G PA +GA S E +L + +GA+ L+ + + Sbjct: 316 KFMEKALARVAKIRQGH-PLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSV 374 Query: 354 DGAAL-----LTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGL 408 L + P L+ EE FGP++ V + A++ AN T YGL AGL Sbjct: 375 LEGELKEGYYMQPTALEGHNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAGL 434 Query: 409 LSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASG----NHR 453 + R + RAG V W + A FGG SG NH+ Sbjct: 435 WTRDGSRAYRCGRAIRAGRV-WTNCYHAYPAHAAFGGYKQSGIGRENHK 482 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: 543 Number of extensions: 31 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