Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 236 bits (602), Expect = 1e-66 Identities = 159/471 (33%), Positives = 236/471 (50%), Gaps = 15/471 (3%) Query: 4 KLLINGELVSGEG-EKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKV 62 K I GE V EG + V NPAT + EI S D AV AA AAF + +T+ Sbjct: 6 KHYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDE 65 Query: 63 RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122 R L + + A+ + G P+ A ++ + + +N L Sbjct: 66 RIALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGI------GHLMSTINALK 119 Query: 123 AGEYLEG-HTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTA 181 A E+ E S++ +P+GVVA I PWN+PL K+APALAAGN +VLKPSE P +A Sbjct: 120 AFEFSEQIGQSLVVHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSA 179 Query: 182 LKLAELA-KDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSI 240 AE+ K PAGV N++ G G VG L+ H V MVS TGS G + + A ++ Sbjct: 180 AIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQVAKNAAETV 239 Query: 241 KRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKL 300 KR H ELGGK+P ++ AD+ V+ N+GQ C A R+ + + Sbjct: 240 KRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIA 299 Query: 301 GAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG---NG 357 + +++G P E +GP+ + A E++ + + G K+ TGG R G Sbjct: 300 SGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEG-AKLETGGPGRPDGIETG 358 Query: 358 YYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGR 417 Y+ PTL +G D I ++E+FGPV+++ P+ +EE+ V AND+ YGL S+V Sbjct: 359 YFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGL-SAVLFGSPEE 417 Query: 418 AHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVR 468 RV+ RL+ G ++N +P GG K SG G++ +GL ++ V+ Sbjct: 418 VKRVAPRLRAGMVYINGG-QPDPSLPFGGYKQSGNGREHGKFGLAEFMEVK 467 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: 525 Number of extensions: 22 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: 474 Length of database: 474 Length adjustment: 33 Effective length of query: 441 Effective length of database: 441 Effective search space: 194481 Effective search space used: 194481 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