Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate GFF3161 PGA1_c32120 aldehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__Phaeo:GFF3161 Length = 485 Score = 204 bits (519), Expect = 6e-57 Identities = 153/459 (33%), Positives = 216/459 (47%), Gaps = 9/459 (1%) Query: 6 IAGQWLA-GQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPA-WARRPLEQRI 63 I G W A G TL +P + DA +DAAV AAR A W +R Sbjct: 16 IDGSWQAPAGGGTLPLTNPSDGSPLCQIARGDARDIDAAVAAARAALDGPWGGMTATERG 75 Query: 64 ELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEKSGP 123 LL R + R D LA++ + GKPL ++ + ++ + A + GE Sbjct: 76 RLLTRMGQMVLERVDTLAQLEAMDVGKPLTQARADAVALARYLEFYGGAADKLHGETIPY 135 Query: 124 LADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTLK 183 A T +PHGV P+N+P + + AL GN V KP+E A Sbjct: 136 QAGYTVYTLREPHGVTGHIVPWNYPMQIIGRSVGAALAMGNACVLKPAEEACLTALAFAH 195 Query: 184 AWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKILA 242 ++AGLPAG LN+V G G E G ALA H G+D + FTGS RTG L+ G + Sbjct: 196 IAVEAGLPAGALNVVPGIGAEAGAALAGHPGVDHISFTGSVRTGALVQQAAGANVVPV-T 254 Query: 243 LEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVAV 302 LE+GG +P +V + ADL+AA+ ++ + +AGQ C+ A R+LV +G + D + A + A Sbjct: 255 LELGGKSPQLVFDDADLEAALPFLVNAGIQNAGQTCSAASRILVQRGVY-DQVRAAMAAA 313 Query: 303 SATLRVGRF--DEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLT 360 + L VG D + P + +L K + I AQ +L+ GA + Sbjct: 314 YSQLTVGPALSDLRLGPLISTRQKEIVEGYLAKGADLAIA--AQGVLSEEASDKGAYVRP 371 Query: 361 PGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFL 420 DV A EE FGP+ +I + D A A+R AN+T YGL AG+ + R + Sbjct: 372 TLFADVGADHPLAQEEIFGPVQVLIPFEDEAEAVRIANSTDYGLVAGIWTRDGARQMRLA 431 Query: 421 VESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYA 459 RAG V N G PFGG+G SG+ R + A Sbjct: 432 KRLRAGQVFLNNYGAGGGVELPFGGVGKSGHGREKGFEA 470 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: 588 Number of extensions: 35 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: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 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 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