Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 232 bits (592), Expect = 2e-65 Identities = 163/475 (34%), Positives = 232/475 (48%), Gaps = 16/475 (3%) Query: 41 YIGGEWVDTK--ERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98 YI G WV + ER+ NP+ S ++ A G AE A+EAA +A+ WK ++R Sbjct: 15 YINGSWVAAQSGERLAVTNPADGSLIIRVPAM-GAAETRQAIEAADRAWGPWKAKTAKER 73 Query: 99 SRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVE 158 S +L + L+ + +L + E GK EA +VA F+E++A A R Y Sbjct: 74 SAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRV-YGDTI 132 Query: 159 VVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAK 218 PG P+G I PWNFP+A+ T +A G V+ KPAED + Sbjct: 133 PEHMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALA 192 Query: 219 VFEIFHEAGFPPGVVNFLP-GVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAP 277 + E+ AGFPPGV N + G + VG L +P+ R ++FTGS EVG + +A Sbjct: 193 LAELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLL------MAQ 246 Query: 278 GQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEP 337 K+ +E GG +V + AD D A G + S Y GQ C A+RL++ G Y+ Sbjct: 247 CAATVKKLSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDA 306 Query: 338 VLERVLKRAERLSVGPAEENP-DLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEGE 395 R+ + L VGP E GP+++ E RKV +I +G ++V+GGKR Sbjct: 307 FTARLAEAVAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKRHARG 366 Query: 396 GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKRE 455 G F PT+ +V P A+EE FGPV + R K EA+ +ANDT +GL YSR Sbjct: 367 GTFFEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVG 426 Query: 456 HLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMK 510 + R G + N + V PFGG K SG + G+ + FLE+K Sbjct: 427 RVWRVSRALEYGIVGINEGLIS--TEVAPFGGVKESGL-GREGSKYGIEDFLEVK 478 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: 625 Number of extensions: 40 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: 485 Length adjustment: 34 Effective length of query: 482 Effective length of database: 451 Effective search space: 217382 Effective search space used: 217382 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