Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_01679 CCNA_01679 succinylglutamic semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__Caulo:CCNA_01679 Length = 485 Score = 471 bits (1213), Expect = e-137 Identities = 244/471 (51%), Positives = 320/471 (67%), Gaps = 7/471 (1%) Query: 3 LWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62 L+I+G W GQGA +P +GE +W A A V A AAR AFP WA ER Sbjct: 5 LFIDGKWRAGQGAGLSSTDPATGEDVWSAATATPADVADAVAAARKAFPAWADRPREERI 64 Query: 63 AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSE 122 A++ R+ +L A ++RETGK WE E+ +M K+ +SI+AY RTG + Sbjct: 65 AILRRYKDILVERAAPYAEALSRETGKALWETRAELASMAGKVDLSIRAYDERTGVTENA 124 Query: 123 MPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMR 182 MP G A LRHR HGV+AV GP+NFPGHLPNGHIVPALLAG+T++FKPSE TP +G+ ++ Sbjct: 125 MPFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLMVE 184 Query: 183 LWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242 + AG P GV+NLVQGGRETGQAL A +D+DGLLFTGSA G R + +P+ ILAL Sbjct: 185 ALEAAGAPAGVVNLVQGGRETGQALIA-QDIDGLLFTGSAAAGTYFRRYFADRPDVILAL 243 Query: 243 EMGGNNPLIIDEVADI-DAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301 E+GGNNPL++ D +A L +QSAF+T GQRC+CARRL++ A G A + VA+ Sbjct: 244 ELGGNNPLVVWNADDAPEAVAALIVQSAFITTGQRCSCARRLIVPDDASGAAIIEATVAL 303 Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLA-PRLLQAGTSLLTP 360 ++RL G W+ E +PF+G LIS +AA+ A + A G+ +LA + G + L P Sbjct: 304 AERLVIGAWNAENEPFMGPLISGRAAK---AAREVASATPGKTILALDGVAGLGDAFLKP 360 Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420 GI+++TG+ PDEE+F PLL+V R +FDEA+ AN TR+GLS GL+S E E +D+ L Sbjct: 361 GIVDVTGLE-TPDEELFAPLLQVRRVSSFDEALAAANATRYGLSAGLISNESELWDKFLS 419 Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLES 471 RAG+VNWN+P TGAA + PFGG+GASGNHRPSA+YAADYCA+P+AS E+ Sbjct: 420 RIRAGVVNWNRPTTGAAGSMPFGGLGASGNHRPSAYYAADYCAYPVASFEA 470 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: 777 Number of extensions: 29 Number of successful extensions: 5 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: 485 Length adjustment: 34 Effective length of query: 458 Effective length of database: 451 Effective search space: 206558 Effective search space used: 206558 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