Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__PV4:5208455 Length = 498 Score = 191 bits (485), Expect = 5e-53 Identities = 146/469 (31%), Positives = 223/469 (47%), Gaps = 18/469 (3%) Query: 5 YIAGQWLAGQG-ETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPA--WARRPLEQ 61 +I G++ A +T + + P+ V+ D + AV ARE F W++ P + Sbjct: 24 FINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGDWSQLPPVK 83 Query: 62 RIELLERFAATLKSRADELARVIGEETGKPL-WESATEVTSMVNKVAISVQAFRERTGEK 120 R +++ RFA L++ DELA + + GKP+ + A +V + S +A + E Sbjct: 84 RKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAVDKIYDEI 143 Query: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAEL 180 + + ++ +P GVVA P+NFP + + PAL GN VV KPSE +P A Sbjct: 144 APTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 203 Query: 181 TLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQK 239 + I+AG+P GVLN++ G G G ALA H +D L FTGS++ L G K Sbjct: 204 MAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESNMK 263 Query: 240 ILALEMGGNNP-LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLAR 298 + LE GG +P +V + +L A + + G+ CT RLLV G + L Sbjct: 264 RVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVKEE--LIN 321 Query: 299 LVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLK------AQEHLIGKGAQPLLAMTQP 352 L+ PA GAV+ E++L+ A+ + +G Q +LA T Sbjct: 322 LIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQQVLAETGG 381 Query: 353 IDGAALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDS 412 + A + + + +A+ EE FGP+L VI + AIR N T YGLAAG+ + Sbjct: 382 VYVAPTIFANVKNEMTIAK---EEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVWTSD 438 Query: 413 RERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461 + + R+G+V W G +APFGG SGN R + +A D Sbjct: 439 ISKAHKTAKALRSGMV-WINHYDGGDMTAPFGGYKQSGNGRDKSLHAFD 486 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: 589 Number of extensions: 30 Number of successful extensions: 7 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: 498 Length adjustment: 34 Effective length of query: 453 Effective length of database: 464 Effective search space: 210192 Effective search space used: 210192 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