Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_089300092.1 CHB84_RS02915 carnitine dehydratase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_900188115.1:WP_089300092.1 Length = 487 Score = 245 bits (625), Expect = 3e-69 Identities = 167/489 (34%), Positives = 245/489 (50%), Gaps = 33/489 (6%) Query: 40 LYIGGEWVDT--KERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFK--TWKDWPQ 95 ++IGG WV++ ER S+NP + A +A+ A+ +A +A + W Sbjct: 1 MFIGGRWVESCSGERFGSVNPYT-GRTWASAPVADEADIHLAVTSAREALEHGPWGRTTA 59 Query: 96 EDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYP 155 DR+R + + A L+ L + GK E S +A D+ Y+A AA + Sbjct: 60 TDRARAMRRLAELIGEHAERLAVAESTDNGKLLREMSGQLAALPDWYHYFAGAADKLHGH 119 Query: 156 AVEVVPYPGEDNESFYV-----PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAE 210 + DN +F+V P+G I PWN P+ + + +A G TV+AKPAE Sbjct: 120 TIPC------DNPNFFVYTRREPIGVVGAIVPWNSPLLLLAWKLAPALAAGCTVVAKPAE 173 Query: 211 DAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYE 270 A V E+ +AG PPGV N + G G GA L HP I FTGS E G + Sbjct: 174 QAPVSTLAFAEVIEQAGIPPGVFNVVTGYGRPAGAELARHPGVDKIAFTGSTETGRSVMT 233 Query: 271 -AAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLI 329 AA +AP +E GGK +V + A+ D A GVV + GQ C A SRL+ Sbjct: 234 GAAEHVAP-------VSLELGGKSPNLVFDDAELDAATNGVVAGIFAAGGQTCMAGSRLL 286 Query: 330 LTQGAYEPVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVL 387 + + Y+ +++R++ RA +++G P + ++GP+ EQ KV YI G+ +G +LV Sbjct: 287 VQESVYDELVDRLVARAGSITLGDPLDPGTEMGPLAFQEQRDKVERYIAEGRRQGARLVC 346 Query: 388 GGKRLEG----EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPY 443 GG + +G F+ PT+FTEV P IA++EIFGPVLSVIR E + VANDT Y Sbjct: 347 GGDAPDDPGLRDGLFVRPTIFTEVSPSMTIARDEIFGPVLSVIRAGTEEEMVRVANDTDY 406 Query: 444 GLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYL 503 GL V+++ H G ++ N + ++ PFGG+KLSG ++ G D L Sbjct: 407 GLAAAVWTQDVRRAHRVADALHAGTVWINAYRSVSV--TTPFGGYKLSGIGSENGQ-DAL 463 Query: 504 RLFLEMKAV 512 + KAV Sbjct: 464 HDYTRTKAV 472 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: 621 Number of extensions: 21 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