Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_012709782.1 NGR_RS27645 aldehyde dehydrogenase family protein
Query= SwissProt::O50174 (487 letters) >NCBI__GCF_000018545.1:WP_012709782.1 Length = 502 Score = 201 bits (510), Expect = 6e-56 Identities = 163/469 (34%), Positives = 236/469 (50%), Gaps = 23/469 (4%) Query: 6 IAGQWLAG-QGETLESLDPVGQGVVWSGRGADATQVDA--AVCAAREAFP--AWARRPLE 60 I GQW+AG +G T+E + P G GVV S R AT VDA A+ AAR AF W R Sbjct: 22 IDGQWMAGAEGRTIERVAP-GHGVVVS-RYQAATMVDAERAIAAARRAFDDGPWPRMTAS 79 Query: 61 QRIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK 120 +R +L R A + +RADELA + E+GKP+ ++ E+ + + RE +GE Sbjct: 80 ERSLILLRAADMIAARADELAYLDAIESGKPISQAKGELAGAADIWRYAAALARELSGES 139 Query: 121 SGPLADAT-AVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAE 179 L + T V+ + GVV++ P+NFP + + + AL AG V KPSELT Sbjct: 140 YNTLGEGTLGVVLREAIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVKPSELTSASTL 199 Query: 180 LTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQ 238 + + AG+PAGV+N++ G G E G LA H +D + FTGS+ G L + Q Sbjct: 200 VLGEILEAAGVPAGVVNIIVGTGPEVGAPLATHPDVDMISFTGSTGIGRLTMAN-AAQTL 258 Query: 239 KILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLAR 298 K ++LE+GG NP +V ADLDA + + A+ +AG+ C RL++ + + + AR Sbjct: 259 KKVSLELGGKNPQIVYPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHRDI-AEEVTAR 317 Query: 299 LVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQ-PIDGAA 357 + ++SA ++VG P +GA+I+ E + G+GA T + Sbjct: 318 ITSLSAKVKVGD-PLDPETQVGAIITPQHLEKIAGYVTAAAGEGAAVSHGGTALDLGMGQ 376 Query: 358 LLTPGILDVSAVAERPD-----EEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDS 412 + P IL A RP+ EE FGP+L V+ + AIR AN+ YGL+AG+ S Sbjct: 377 FMAPTILS----AVRPEMAVAREEVFGPVLSVLTFETTEEAIRIANSIDYGLSAGVWSRD 432 Query: 413 RERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461 + RAG V W A PFGG SG R +A + Sbjct: 433 FDTCLTIGRRVRAGTV-WMNTFMDGACELPFGGYRQSGLGRELGRHAVE 480 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: 585 Number of extensions: 39 Number of successful extensions: 8 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: 502 Length adjustment: 34 Effective length of query: 453 Effective length of database: 468 Effective search space: 212004 Effective search space used: 212004 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