Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= SwissProt::O50174 (487 letters) >FitnessBrowser__BFirm:BPHYT_RS23175 Length = 497 Score = 202 bits (515), Expect = 2e-56 Identities = 157/470 (33%), Positives = 235/470 (50%), Gaps = 21/470 (4%) Query: 5 YIAGQWLAGQG-ETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPA--WARRPLEQ 61 +I G++ +G T + L P+ ++ + A VDAAV AAR AF + W+ Q Sbjct: 23 FIDGEYRDAEGGRTFDCLSPIDGKLLAKVADSGAADVDAAVAAARRAFDSGVWSGLNPRQ 82 Query: 62 RIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSM-VNKVAISVQAFRERTGEK 120 R +L R+AA+++ DELA + + GKP+ + TS+ V A V+ F E + Sbjct: 83 RKAVLLRWAASIREHMDELALLETLDAGKPI----ADTTSVDVPGAAYCVEWFAEAIDKI 138 Query: 121 SGPLADAT----AVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPK 176 G +A A ++ +P GVVA P+NFP + + PAL AGN VV KPSE +P Sbjct: 139 GGEVAPADHHLLGLVTREPIGVVAAVVPWNFPILMASWKFGPALAAGNSVVLKPSEKSPL 198 Query: 177 VAELTLKAWIQAGLPAGVLNLVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQ 236 A + + AG+PAGV N+V G E G LA H+ +D L FTGS+ G L+ G Sbjct: 199 TAIRLAQLALDAGIPAGVFNVVPGAGEPGKLLALHQDVDCLAFTGSTNVGKLIMQYAGQS 258 Query: 237 PQKILALEMGGNNP-LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDAL 295 K + LE+GG +P +V+ + D+D A + F + G+ CT RLLV + D Sbjct: 259 NLKRVWLELGGKSPNIVMPDCPDMDRAANAAAGAIFYNMGEMCTAGSRLLVHRDI-KDVF 317 Query: 296 LARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLL---AMTQP 352 + +L+A + + G P MGA++ E +L E G+ LL A + Sbjct: 318 IDKLIAAARSYTPGN-PLDPDTSMGAIVDKVQLERVLGYIE--AGRAEAKLLLGGARVKE 374 Query: 353 IDGAALLTPGILDV-SAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSD 411 G + P I ++ + A+ EE FGP+L VI + AIR AN ++YGLAA + + Sbjct: 375 DTGGFYIEPTIFEIPGSGAKVAREEIFGPVLSVITFDTVEEAIRIANDSEYGLAAAVWTS 434 Query: 412 SRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461 + + + RAG V N G + PFGG SGN R + +A + Sbjct: 435 NLTTAHEVSRKLRAGTVWVNCYDEGGDMNFPFGGYKQSGNGRDKSLHALE 484 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: 581 Number of extensions: 30 Number of successful extensions: 5 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: 497 Length adjustment: 34 Effective length of query: 453 Effective length of database: 463 Effective search space: 209739 Effective search space used: 209739 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