Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Ga0059261_1006 Ga0059261_1006 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Korea:Ga0059261_1006 Length = 453 Score = 198 bits (504), Expect = 3e-55 Identities = 146/459 (31%), Positives = 210/459 (45%), Gaps = 14/459 (3%) Query: 55 SLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKR 114 S+NP A E T A EAAL A AF++W+ R+ LL A KR Sbjct: 4 SINP-ATGEAGATFAALDDDAIEAALTRAEAAFRSWRASDIAQRTALLTAIADRFEANKR 62 Query: 115 ELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPL 174 L T E+GK A A+V + I +YA Y P +E G ++PL Sbjct: 63 HLAETATKEMGKTLASAIAEVEKCIAGFRHYADKGPGYLAP-IETKTASGRA-VGHWLPL 120 Query: 175 GAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVN 234 G + + PWNFP + + GN + K A A + ++ AG P G+ Sbjct: 121 GPILAVMPWNFPYWQVVRWLAPTILAGNVGLLKHASLTQGCAALIQQMVSAAGAPDGLFQ 180 Query: 235 FLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDA 294 LP ++V + + R + TGS G K+ EAAGR K+ +E GG D Sbjct: 181 NLPIKSDKVSRIIAD-TRVAAVTLTGSEGAGAKVAEAAGRA------LKKVVLELGGSDP 233 Query: 295 IIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVG-P 353 IV +AD D A V + GQ C A R+I+ Y+ L++ + +G P Sbjct: 234 FIVMPSADLDKAVATAVKARVQNAGQSCICAKRMIVHADVYDAFLDKFTAAMLAVKIGDP 293 Query: 354 AEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARI 413 E+ ++GP+ S EQ VL +E +G + GG ++E +G ++ V T V P A Sbjct: 294 MEDGVEMGPLSSVEQRDTVLEQVERAVADGATLAGGAKIERDGAWMEAGVLTHVHPDADF 353 Query: 414 AQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNR 473 AQEEIFGPV V R D A+ +AND P+GL V++ + ++ R+ G N+ Sbjct: 354 AQEEIFGPVAMVFRADDIDAAIALANDVPFGLGSSVWTSDQAEIDRFVRDIESGMTAVNQ 413 Query: 474 KITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAV 512 + A PFGG KLSG + G L F+ +KAV Sbjct: 414 LL--ASTPEAPFGGVKLSGHGRELGPWG-LHEFMNLKAV 449 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: 480 Number of extensions: 28 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: 516 Length of database: 453 Length adjustment: 34 Effective length of query: 482 Effective length of database: 419 Effective search space: 201958 Effective search space used: 201958 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 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