Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BWI76_RS11680 BWI76_RS11680 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__Koxy:BWI76_RS11680 Length = 492 Score = 784 bits (2024), Expect = 0.0 Identities = 384/489 (78%), Positives = 424/489 (86%) Query: 1 MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60 M+LWINGDW +G+G +R K NPVS +LWQGNDADA QV A AARAAFP WAR FA Sbjct: 1 MSLWINGDWQSGRGPARSKHNPVSQTLLWQGNDADADQVALAVSAARAAFPAWARQPFAA 60 Query: 61 RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120 R A+ E+FA+LLE+NK+ELTA+IARETGKPRWEAATE+TAMINKIAIS+ AYH RTGE + Sbjct: 61 RKAIAEKFASLLEANKSELTAVIARETGKPRWEAATEITAMINKIAISVNAYHSRTGEAQ 120 Query: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180 + M DG A+LRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNT++FKPSELTP SGEAV Sbjct: 121 TAMADGEATLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPQSGEAV 180 Query: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240 ++LW +AGLPPGVLNL+QGGRETG+ALS D+DGLLFTGS+ TG+QLHRQL+GQPEKIL Sbjct: 181 VKLWAEAGLPPGVLNLLQGGRETGEALSGQADIDGLLFTGSSATGFQLHRQLAGQPEKIL 240 Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300 ALEMGGNNPLI+D+ DIDAAVHLTIQSAF+TAGQRCTCARRLL+K G GDAFL RLV Sbjct: 241 ALEMGGNNPLIVDDPQDIDAAVHLTIQSAFITAGQRCTCARRLLVKRGEAGDAFLQRLVT 300 Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360 VSQ L P WD EPQPFIGGLIS QAAQ+V AW A GG+ LL PRLLQAGTSLLTP Sbjct: 301 VSQTLIPAAWDAEPQPFIGGLISAQAAQKVHQAWLAHVASGGKTLLEPRLLQAGTSLLTP 360 Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420 GIIEM+ VA V DEEVFGPLL VWRYD FDEAI +AN TRFGLSCGL+S ER+KFDQLLL Sbjct: 361 GIIEMSAVAQVADEEVFGPLLCVWRYDHFDEAIALANATRFGLSCGLISAERDKFDQLLL 420 Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480 EARAGIVNWNKPLTGAASTAPFGG GASGNHRP AWYAADYCAWPMASLES L+LPATL Sbjct: 421 EARAGIVNWNKPLTGAASTAPFGGTGASGNHRPGAWYAADYCAWPMASLESPELSLPATL 480 Query: 481 NPGLDFSDE 489 +PGL+F E Sbjct: 481 SPGLNFRQE 489 Lambda K H 0.318 0.134 0.412 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: 949 Number of extensions: 38 Number of successful extensions: 1 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: 492 Length of database: 492 Length adjustment: 34 Effective length of query: 458 Effective length of database: 458 Effective search space: 209764 Effective search space used: 209764 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