Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate BPHYT_RS28770 BPHYT_RS28770 aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__BFirm:BPHYT_RS28770 Length = 480 Score = 275 bits (703), Expect = 3e-78 Identities = 174/456 (38%), Positives = 256/456 (56%), Gaps = 19/456 (4%) Query: 41 YIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSR 100 ++GGEWVD + ++NPS S+V+G A+A + + A+ +A AF+TW + R Sbjct: 7 FVGGEWVDGNDFAPNVNPSDTSDVIGHFARASADQTQKAIASARSAFRTWSLSTPQQRFD 66 Query: 101 LLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVV 160 LL +A + + RK EL L E GK EA +V A +++A ALR E++ Sbjct: 67 LLDQAGSTILARKNELGKLLAREEGKTLAEAVGEVGRAGQIFKFFAGEALRV---GGEIL 123 Query: 161 PY--PGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGA- 217 P PG E P+G +I PWNFP+AI I +A GN V+ KPAE +V G+ Sbjct: 124 PSVRPGLTVEVTREPVGVIGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAE--LVPGSV 181 Query: 218 -KVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276 ++ +I EAG P GV+N + G+G VG LV ++FTGS+ G I AA +A Sbjct: 182 WELVKIIAEAGAPAGVINLVMGMGSIVGEILVMSADVDAVSFTGSVGTGQAI--AAKCVA 239 Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336 G K+ +E GGK+ ++V + AD D+A E + A+ GQ+C+A+SRLI+T G ++ Sbjct: 240 TG----KKFQLEMGGKNPMVVLDDADLDVAVEACINGAFYSTGQRCTASSRLIVTSGIHD 295 Query: 337 PVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEG- 394 +E +L R L +G A + + +GPVV A+Q + YIE+ +NEG V GG+R+ Sbjct: 296 RFVEAMLARMRSLKIGNALDASTQIGPVVDAKQLEQDERYIELARNEGGSVFGGERVTSA 355 Query: 395 -EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRK 453 EG+F+AP + T P I +EE+FGPV SVI+V ++ EAL VAND+P+GL+ G+ + Sbjct: 356 TEGFFLAPALVTNTTPAMTINREEVFGPVASVIKVANYEEALAVANDSPFGLSAGICTMS 415 Query: 454 REHLEWARREFHVGNLYFNRKITGALVGVQPFGGFK 489 H +R G + N G V PFGG K Sbjct: 416 LAHASHFKRHVQAGMVMINTATAGVDYHV-PFGGRK 450 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: 633 Number of extensions: 36 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: 480 Length adjustment: 34 Effective length of query: 482 Effective length of database: 446 Effective search space: 214972 Effective search space used: 214972 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