Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate RR42_RS27350 RR42_RS27350 aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Cup4G11:RR42_RS27350 Length = 486 Score = 258 bits (658), Expect = 4e-73 Identities = 157/465 (33%), Positives = 239/465 (51%), Gaps = 24/465 (5%) Query: 41 YIGGEWVDTKERMV--SLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98 YI GEW + ++NP+ +++VG + +A+AA+ AA AF WK P R Sbjct: 12 YINGEWSKSASGRTFDNVNPADTADIVGRFQASTADDAQAAVAAAAAAFDAWKKTPISKR 71 Query: 99 SRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVE 158 +++L AA + ++ L E GK + +V + I +YA + Sbjct: 72 AKILNGAADYLEANAEQIAEELTREEGKALNLSKDEVLRSAQTIRFYAVEGQSFSGET-- 129 Query: 159 VVPYPGEDNESFYV----PLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVV 214 YP +D + PLG VI+PWNFPV+I I + GNTV+ KP+ DA + Sbjct: 130 ---YPQDDPDMIVYSQREPLGVVTVISPWNFPVSIPARKIAPALIAGNTVVFKPSSDAPL 186 Query: 215 VGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGR 274 G ++ + F EAG P GV+NF+ G +VGA + E P R I+FTGS G I+ + Sbjct: 187 SGYRLAQAFVEAGIPKGVLNFITGRAGDVGAAITEAPAVRAISFTGSTAAGQHIHRSV-- 244 Query: 275 LAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGA 334 + R +E GGK+ +IV E AD D A + + GQ C+ SR+++ Sbjct: 245 -----SLSTRTQMELGGKNPLIVMEDADLDRAVDLTIKGGLSLSGQACTGTSRVLVMASV 299 Query: 335 YEPVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLE 393 E++L + + L +G D+GP+ + +Q VL Y+E GK+E + GG RL Sbjct: 300 KAAYTEKLLAKVKTLKIGSGMTPGMDVGPLATRKQLETVLGYVEAGKSEATHLCGGDRLG 359 Query: 394 GE----GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGV 449 GE G++++P VFT V + RIA+EEIFGPV+++I V +A+A+ ANDT YGL+ + Sbjct: 360 GEPYDKGFYVSPAVFTGVTQQMRIAREEIFGPVIAIIEVSSYADAIAKANDTEYGLSAAI 419 Query: 450 YSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTN 494 + + + G + NR TG L+ PFGG K S T+ Sbjct: 420 VTSNPRYAHDFAHDIQSGTVKINRTTTGNLINA-PFGGLKQSSTS 463 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: 584 Number of extensions: 41 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 516 Length of database: 486 Length adjustment: 34 Effective length of query: 482 Effective length of database: 452 Effective search space: 217864 Effective search space used: 217864 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