Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Dyella79:N515DRAFT_3729 Length = 483 Score = 231 bits (588), Expect = 6e-65 Identities = 174/480 (36%), Positives = 247/480 (51%), Gaps = 28/480 (5%) Query: 50 KERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALM 109 +ER + + A EV ++ A+ +AA+ AA A W P E R+RLL + A L+ Sbjct: 19 QERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRARLLQRLADLI 78 Query: 110 RRRKRELEATLVYEVGKNWVEA-SADVAEAIDFIEYYARAALRYRYP--AVEVVPYPGED 166 R E A + GK A S D+ A+ + Y+A A + + A+E+ G Sbjct: 79 EARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSESHAMEL----GAI 134 Query: 167 NESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEA 226 N + PLG I+PWN P+ +FT I +A GN V+AKP+E A + E+ EA Sbjct: 135 NYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAALLGELSIEA 194 Query: 227 GFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAY 286 GFPPGV+N + G G EVG LVEH + ++FTGS G +I AA AP FK+ Sbjct: 195 GFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAA---APR---FKKLS 248 Query: 287 VETGGKDAIIVDETADF-DLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKR 345 +E GGK+ IV AD D + +V S + QG+ C SRL++ + Y+ ER L + Sbjct: 249 LELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYLAK 308 Query: 346 AERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVL-GGKRLE-----GEGYF 398 L VG P E DLG +VS E KV I + EG VL GG L G++ Sbjct: 309 VRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALPGPLAGGWY 368 Query: 399 IAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR--KREH 456 +APTV + P+ Q+EIFGPV+++I D A+AL +AN T YGL +++ R H Sbjct: 369 VAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSRAH 428 Query: 457 LEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF 516 A+ +F G ++ N + L PFGG K SG + G ++ LR F E K + R+ Sbjct: 429 RFGAQLDF--GIVWINCWLLRDL--RTPFGGAKQSGV-GREGGVEALRFFTEPKNICIRY 483 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: 565 Number of extensions: 31 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: 483 Length adjustment: 34 Effective length of query: 482 Effective length of database: 449 Effective search space: 216418 Effective search space used: 216418 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