Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 194 bits (492), Expect = 7e-54 Identities = 163/489 (33%), Positives = 225/489 (46%), Gaps = 32/489 (6%) Query: 2 STHYIAGQWLAGQGETLESLD-PVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLE 60 S YI GQW+A G ++ P + V+ AT D A AA AFPAWA Sbjct: 5 SRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGA 64 Query: 61 QRIELLERFAATLKSRADELARVIGEETGKPLW-----ESATEVTSMVNKVAISVQAF-R 114 +R L++ A LK+R DEL R+I E G P+ ++ + + I+ + F Sbjct: 65 ERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAEGFAE 124 Query: 115 ERTGEKSGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELT 174 ER G+ +++ P G VA P+NFP H + AL AG VV KPSE+ Sbjct: 125 ERIGQ---------SLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVA 175 Query: 175 PKVAELTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQF 233 P A L + AGLPAGV NLV G G G ALAAH L + FTGS+ G + + Sbjct: 176 PLNAFLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRV-AAV 234 Query: 234 GGQPQKILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGD 293 K ++LE+GG + VV ADL AAV + F+++GQ C+ RLLVPQ + + Sbjct: 235 AAATVKRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAE 294 Query: 294 ALLARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLL---AMT 350 A + A +A E +G ++S + + E + GA+ L A Sbjct: 295 AAALAVQAAAAYTLGDPLAE--GSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAP 352 Query: 351 QPIDGAALLTPGILD-VSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLL 409 + + + P + V A EE FGP+L ++ Y D A A AN T YGLAA + Sbjct: 353 EGLPTGYYVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVW 412 Query: 410 SDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAADYCAYPVAS 469 S R F RAG V+ N APFGG SG R + + Sbjct: 413 SAEEARALAFARRLRAGQVDINGAFFNLL--APFGGFKQSGYGRELGRHGVE------DF 464 Query: 470 LESPSVSLP 478 LE+ S+ LP Sbjct: 465 LETQSIQLP 473 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: 598 Number of extensions: 32 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: 476 Length adjustment: 34 Effective length of query: 453 Effective length of database: 442 Effective search space: 200226 Effective search space used: 200226 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