Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 210 bits (535), Expect = 7e-59 Identities = 137/455 (30%), Positives = 227/455 (49%), Gaps = 12/455 (2%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 NP TG+ + A+ +V A+ A A F W R + L K AD++ E+ +A Sbjct: 7 NPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQYA 66 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSM----IRRDP 138 ++ + GK + A E+ + ++A A L LA + H S + P Sbjct: 67 KVLTLEMGKVIGEA-EGEVELCAQILEYYADHAEQL--LAPEKLSSRHPSYTQSWVEHVP 123 Query: 139 LGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGVI 197 G++ ++ PWN+P AP LAAGN ++LK + P A L ++ P G Sbjct: 124 QGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGGF 183 Query: 198 NILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVFD 257 L+ + + P+V+ V+LTGS G + + ++K++ MELGG +V Sbjct: 184 TNLYATRDQL-KAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAFVVLA 242 Query: 258 DADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDEST 317 DAD++ V+ T ++NAGQ C ++ RI IYD +EK A VA L++G P + ST Sbjct: 243 DADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEPST 302 Query: 318 ELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAIVQK 377 L P+SS ++ + K +E+A A G KV G + G ++ P LL+ D+ Sbjct: 303 TLAPMSSRGAVDDLKKQLEQAVAHG-AKVEVIGAEVPSRGAFFRPVLLSHVSDDNPARYW 361 Query: 378 EVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFM 437 E FGPV V +E + ANDS +GL SV+T D+ V+ ++ G ++N Sbjct: 362 EFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYINHPTG 421 Query: 438 LVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 + +++P GG + SGYG++++ G++++ V H ++ Sbjct: 422 VAADLPFGGVRRSGYGRELTGLGIKEF--VNHKLI 454 Lambda K H 0.317 0.134 0.397 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: 472 Number of extensions: 23 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: 474 Length of database: 463 Length adjustment: 33 Effective length of query: 441 Effective length of database: 430 Effective search space: 189630 Effective search space used: 189630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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