Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3096 HP15_3039 N-succinylglutamate 5-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >lcl|FitnessBrowser__Marino:GFF3096 HP15_3039 N-succinylglutamate 5-semialdehyde dehydrogenase Length = 491 Score = 594 bits (1531), Expect = e-174 Identities = 287/484 (59%), Positives = 369/484 (76%), Gaps = 1/484 (0%) Query: 3 LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62 L+I+G W+ G G PV+GE LW G A+ V+ A R AR AF +W R SFAER Sbjct: 8 LFIDGLWLPGHGPVFESVQPVTGETLWDGESANLEDVDAAVREARNAFVKWQRKSFAERQ 67 Query: 63 AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSE 122 AVVE F LLE++K EL I ETGKP WE+ TEV AMI KI IS+KAY+ RTG S+ Sbjct: 68 AVVEAFGELLEAHKEELAHQIGLETGKPLWESRTEVAAMIGKIGISVKAYNDRTGTSESD 127 Query: 123 MPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMR 182 + G A LRHRPHGV+AVFGPYNFPGHLPNGHIVPALLAGNT++FKPSELTP E ++ Sbjct: 128 VAGGHAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPGVAELTVK 187 Query: 183 LWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242 LW +AG+P GV+NLVQG TG++L+ +DGL FTGS+ G+ LH+Q GQPEKI+AL Sbjct: 188 LWGKAGIPDGVINLVQGASATGKSLAGHPLIDGLFFTGSSTVGHLLHKQFGGQPEKIVAL 247 Query: 243 EMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVS 302 EMGGNNPLI+ +VAD+D AVH +QSAF++AGQRCTCARRLL+ G +GDAF+ RLV VS Sbjct: 248 EMGGNNPLIVQDVADVDGAVHHALQSAFLSAGQRCTCARRLLVPKGKKGDAFIDRLVEVS 307 Query: 303 QRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTPGI 362 R+ G +D +PQPF+G +IS +AA++++ A L GG+ LL + L++GT LL+PGI Sbjct: 308 ARIKVGEFDADPQPFMGSVISSEAAEKLLAAQASLLEKGGKSLLEMKSLKSGTGLLSPGI 367 Query: 363 IEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEA 422 ++ TG+ V DEE FGPLL+V+RY +FD+A+ +AN+T +GLS G+++ +R+ +++L+ E Sbjct: 368 VDATGL-DVTDEEFFGPLLKVYRYKSFDDALALANDTHYGLSAGILTDDRKLYERLVEEV 426 Query: 423 RAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATLNP 482 RAGIVNWN+PLTGA+S APFGG+GASGNHRPSA+YAADYCAWPMASLE+ +P +L P Sbjct: 427 RAGIVNWNRPLTGASSAAPFGGVGASGNHRPSAYYAADYCAWPMASLEAGKSEMPESLAP 486 Query: 483 GLDF 486 GL+F Sbjct: 487 GLNF 490 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: 833 Number of extensions: 32 Number of successful extensions: 2 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: 491 Length adjustment: 34 Effective length of query: 458 Effective length of database: 457 Effective search space: 209306 Effective search space used: 209306 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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