Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_059151695.1 V474_RS11820 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >NCBI__GCF_001046635.1:WP_059151695.1 Length = 474 Score = 456 bits (1172), Expect = e-132 Identities = 230/453 (50%), Positives = 309/453 (68%), Gaps = 4/453 (0%) Query: 21 NPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVVERFAALLESNKAELT 80 +P +GE +W+G A V A AR AFP WA L AER A +R+ A LE+ K + Sbjct: 8 DPATGETVWEGEIAGPQAVSAALLRARKAFPAWAALPVAERVAAAQRYKAALEARKDAIA 67 Query: 81 AIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPDGAASLRHRPHGVLAV 140 IIARETGKP WE TEV +MI K+ +SI A R G+++S MP G A LRHRPHGV+AV Sbjct: 68 QIIARETGKPMWETRTEVASMIGKVGLSITAQAERAGDRQSAMPFGQAVLRHRPHGVMAV 127 Query: 141 FGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRLWQQA-GLPPGVLNLVQG 199 GP+NFPGHLPNGHIVPAL+AGNT++FKPSE+TP +G A+ W +A V +QG Sbjct: 128 LGPFNFPGHLPNGHIVPALIAGNTVVFKPSEMTPATGAAMAECWAEALADHRHVFQCIQG 187 Query: 200 GRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILALEMGGNNPLIIDEVADID 259 RETG+AL A +DGLLFTGSA G R + +P+ ILALE+GGNNPLI + AD+D Sbjct: 188 ARETGEALVA-GHIDGLLFTGSAGAGAHFRRIFADRPDVILALELGGNNPLIAWDSADVD 246 Query: 260 AAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAVSQRLTPGNWDDEPQPFIG 319 A + +QS F+T GQRC+CARRL++ A G A + + ++ R+ G W++ P+P+IG Sbjct: 247 EAASVVVQSGFITTGQRCSCARRLIVPDNAFGAALVDAVAGLADRIVIGAWNETPEPWIG 306 Query: 320 GLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGT-SLLTPGIIEMTGVAGVPDEEVFG 378 LIS+ AAQ + +L G + + ++ + + +TP I+++TG+ VPDEE+F Sbjct: 307 PLISDAAAQAAKARFAELVERGAKVIRPLNGVEGRSGAFVTPAILDVTGIF-VPDEEIFA 365 Query: 379 PLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLLEARAGIVNWNKPLTGAAS 438 P+L++ R FD AI ANNTRFGLS GL+S + + ++L+E RAG+VN N+P TGAA Sbjct: 366 PVLQISRVPDFDAAIEAANNTRFGLSAGLISADDALWQRVLVEGRAGVVNRNRPTTGAAG 425 Query: 439 TAPFGGIGASGNHRPSAWYAADYCAWPMASLES 471 + PFGG+G SGNHRPSA+YAADYCA+P+AS E+ Sbjct: 426 SMPFGGLGESGNHRPSAYYAADYCAYPVASFEA 458 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: 774 Number of extensions: 41 Number of successful extensions: 4 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: 474 Length adjustment: 34 Effective length of query: 458 Effective length of database: 440 Effective search space: 201520 Effective search space used: 201520 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 24 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