Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_104912863.1 C3B54_RS01080 aldehyde dehydrogenase family protein
Query= BRENDA::Q65NN2 (516 letters) >NCBI__GCF_002950575.1:WP_104912863.1 Length = 1180 Score = 227 bits (579), Expect = 2e-63 Identities = 141/432 (32%), Positives = 222/432 (51%), Gaps = 24/432 (5%) Query: 77 EKAIQAAAKAFETWRYTDPEERAAVLFRAVAKVRRKKHEFSALLVKEAGKPWNEADADTA 136 + ++ + + W E R +L +A A++ ++ E +++++EAGK E+D + + Sbjct: 546 DSIVEKMRRGGKKWAARGAEGRGKILLKAAAELGVRRGEIMSVMMQEAGKTLAESDPEIS 605 Query: 137 EAIDFMEYYARQMIELAKGKPVNSREGERNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAP 196 EAIDF YYA Q +E+ + N +TP G+T+V PPWNF AI G+ + Sbjct: 606 EAIDFARYYASQAVEME----------QLNGAKFTPVGLTMVAPPWNFPVAIPTGSVTSA 655 Query: 197 IVTGNTVVLKPASAAPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSIIT 256 + G+ V++KPA AA VE L +G+PK V++ S E+G L+ H + Sbjct: 656 LAAGSAVIIKPAPQVRRCAAVMVEALWAAGVPKDVLHLADVSEGELGRALISHQGVDRVI 715 Query: 257 FTGSREVGTRIFERAAKVQPGQTHLKQVIAEMGGKDTVVVDEDCDIELAAQSIFTSAFGF 316 TG+ FE AA + + L V+AE GK+ +V+ DI+LA + SAFG Sbjct: 716 LTGA-------FETAALFRSWRADL-PVLAETSGKNALVITPSADIDLAVADLVKSAFGH 767 Query: 317 AGQKCSAGSRAVVHEKV--YDEVLKRVIEITESKKVGEPDS-ADVYMGPVIDQASFNKIM 373 AGQKCSA S ++ V + +++ + + VG PD+ + M P+I+ Sbjct: 768 AGQKCSAASLVILVGSVAKSERFWRQLEDAVNTLDVGWPDARPETTMNPIIEPPGAKLRQ 827 Query: 374 DYIEIGKEEGRLVSGGKGDDSKGYFIEPTIFADLDPKARLMQEEIFGPVVAFSKVSSFDE 433 E+G E L + DD++ + P + + P + Q E FGP++ + + Sbjct: 828 GLTELGAGEEWLAEPRQLDDTERLW-SPGVRLGVRPGSTFHQTEYFGPLLGVMTARTLQD 886 Query: 434 ALEVANNTEYGLTGAVITKNRDHINRAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMS-- 491 A+E N+ EYGLT + + + D ++ H GNLY NR TGAIV PFGG+K S Sbjct: 887 AVEYQNSVEYGLTAGIHSLDPDEVSYWLDHVHAGNLYVNRGITGAIVRRQPFGGWKKSSV 946 Query: 492 GTDSKAGGPDYL 503 G +KAGGP+YL Sbjct: 947 GPTAKAGGPNYL 958 Lambda K H 0.315 0.133 0.382 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: 1204 Number of extensions: 56 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: 516 Length of database: 1180 Length adjustment: 41 Effective length of query: 475 Effective length of database: 1139 Effective search space: 541025 Effective search space used: 541025 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 (21.6 bits) S2: 55 (25.8 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