Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate GFF4005 HP15_3945 aldehyde dehydrogenase family protein
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__Marino:GFF4005 Length = 471 Score = 190 bits (483), Expect = 8e-53 Identities = 145/460 (31%), Positives = 229/460 (49%), Gaps = 23/460 (5%) Query: 1 MSTHYIAGQWLAGQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLE 60 ++ +YI GQW++ G+ ++ + V+ A A +++ A+ AA AF +W+ LE Sbjct: 4 LNRNYINGQWVSWAGDMIDVHEAGTGDVIARVPAAGADEMEQAIAAADAAFESWSESTLE 63 Query: 61 QRIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK 120 +RI++LE+ A LK RA E+A + E G P+ + AT + A +++ + + Sbjct: 64 ERIKVLEQLHAGLKERAPEIAETVCREVGMPI-KLATPI--QAGMPAAVTKSYLKLLPDF 120 Query: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAEL 180 + +++ P GVV P+N+P H IVPA+ AG VV KPSE+ P+ A + Sbjct: 121 PFTEQSGNSEVQYAPVGVVGCITPWNYPLHQVILKIVPAIAAGCTVVLKPSEIAPQTAFI 180 Query: 181 TLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQK 239 + LP GV N+V G G G L H + + FTGS+RTGNL+ + K Sbjct: 181 LAEILDGTDLPKGVFNMVCGYGHTVGDTLIKHPDVRMVSFTGSTRTGNLI-AHAAADDFK 239 Query: 240 ILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARL 299 ALEMGG + V+ ADL AAV I + +++GQ CT R+LVP +A Sbjct: 240 RFALEMGGKSASVILPDADLAAAVKGTINNCLLNSGQTCTALTRMLVPADKHDEACELAA 299 Query: 300 VAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGA--- 356 AV+ +E +G + S + ++ + + +GA+ + + +G Sbjct: 300 AAVAKMTPGNPLEETTR--LGPLSSAQQRDKVIDYIKLGVQEGAKLIAGGPEAPEGCEKG 357 Query: 357 ----ALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDS 412 A + + S +A+ EE FGP+L VI Y+D A A++ AN TQYGL+ + S Sbjct: 358 YFVKATVFGNVKPDSRIAQ---EEIFGPVLCVIPYNDEAEAVKIANGTQYGLSGAVWSGD 414 Query: 413 RERFEQFLVESRAGIVNWNKQLTGAASS--APFGGIGASG 450 + ++ + R G V N G A + APFGG G SG Sbjct: 415 DAKAKKIASKLRTGQVFVN----GGAFNPMAPFGGFGHSG 450 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: 565 Number of extensions: 25 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: 471 Length adjustment: 34 Effective length of query: 453 Effective length of database: 437 Effective search space: 197961 Effective search space used: 197961 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