Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_028584773.1 G494_RS0112240 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000429965.1:WP_028584773.1 Length = 487 Score = 224 bits (570), Expect = 7e-63 Identities = 152/476 (31%), Positives = 224/476 (47%), Gaps = 16/476 (3%) Query: 37 HYPLYIGGEWVDTKE-RMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQ 95 H +I G+W+D + ++ A EV+ A+ G AE A+EAA A W+ P Sbjct: 11 HDQAFINGDWLDADSGETLEVHNPASGEVIAAIARCGSAETRRAIEAAEAALPDWRARPA 70 Query: 96 EDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYP 155 ++R++LL L+ + +L L E+GK EA ++A ++IE++A A R Y Sbjct: 71 KERAKLLRSWFNLLMAHQEDLAKILTAEMGKPLAEARGEIAYGANYIEWFAEEAKRV-YG 129 Query: 156 AVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVV 215 P G+ P+G I PWNFP A+ T I +AVG TV+ KPA + Sbjct: 130 DTIPAPDKGKRLVCIKQPVGVVACITPWNFPNAMLTRKIAPALAVGCTVVCKPANATPLS 189 Query: 216 GAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRL 275 + E+ AG P GV+N L G E+G L +P R + FTGS VG ++ A Sbjct: 190 ALALAELATRAGIPAGVINILGGKTPEIGKELTSNPLVRKLTFTGSTPVGKELMAACSAT 249 Query: 276 APGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAY 335 K+ +E GG IV AD D A EG + S Y GQ C ++R+++ + Y Sbjct: 250 V------KKTSMELGGNAPFIVFADADLDAAVEGAIASKYRNAGQTCVCSNRILVQEEIY 303 Query: 336 EPVLERVLKR-AERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRL 392 + E++ L +G +E GP++ VL+ IE +G Q++LGG + Sbjct: 304 DAFAEKLAAAVGGNLVLGNGMDEGVTTGPLIDETAAENVLAIIEDAVEKGAQVILGGGQP 363 Query: 393 EGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452 G F+ PT+ T V R+ +EEIFGPV + EA+ +ANDT +GL Y+R Sbjct: 364 ALGGSFVEPTILTRVDETMRVYREEIFGPVAPLFAFSTEEEAIAMANDTEFGLAAYFYAR 423 Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGT---NAKTGALDYLRL 505 + G + N I PFGG K SG +K G DYL + Sbjct: 424 DIGRIWRVSEALEYGIVGINEGIISN--ETAPFGGVKESGNGREGSKYGLDDYLEI 477 Lambda K H 0.319 0.137 0.403 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: 592 Number of extensions: 28 Number of successful extensions: 4 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: 516 Length of database: 487 Length adjustment: 34 Effective length of query: 482 Effective length of database: 453 Effective search space: 218346 Effective search space used: 218346 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 24 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