Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_083831993.1 AZO_RS11360 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000061505.1:WP_083831993.1 Length = 478 Score = 336 bits (861), Expect = 1e-96 Identities = 189/468 (40%), Positives = 270/468 (57%), Gaps = 15/468 (3%) Query: 16 GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAF--AEWGQTTPKVRAECLLKLADV 73 GE V +PATG + A +D AV AA AF EW + P R LLK AD+ Sbjct: 13 GETLAVLDPATGQAFATVPAGGAADIDRAVAAARRAFESGEWPKMRPVDRERLLLKFADL 72 Query: 74 IEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG--------LAAGE 125 IE N Q AE+E+ + GKP+ A + ++ +VD R+ AG A + G L Sbjct: 73 IEANAQELAEIEALDNGKPVMMARHVDVALVVDFLRYMAGWATKIEGSTMDVSVPLMRDR 132 Query: 126 YLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185 L G T RR+P+GVV +I PWN+PL+MAAWK+ PAL +G +VLKP+E TPLTAL+ A Sbjct: 133 ELFGFT---RREPVGVVGAIIPWNFPLLMAAWKVGPALTSGCTMVLKPAEETPLTALRFA 189 Query: 186 ELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244 ELA + +PAGV+N++ G G T G L H + V+ TGS G+ + ++ R Sbjct: 190 ELALEAGYPAGVLNVVTGHGDTAGAALASHKGIEKVAFTGSTEIGKLVGKAAIDNMTRVS 249 Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304 +ELGGK+PVIV DDAD G ++N GQ CTA R++ K ++ +VE L Sbjct: 250 LELGGKSPVIVLDDADPAMAAAGAAQAIFFNQGQVCTAGSRLFIHKSRFEKVVEGLSGIA 309 Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364 A++K G D ST++GPL S +RV +E A G + TGG GY+ PT+ Sbjct: 310 ASMKLGPGIDPSTQIGPLVSAVQQQRVLGYIESGLAEG-ARAATGGGAGGEAGYFVKPTV 368 Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424 L A +V++E+FGPVV P+++ ++V + AND+ YGLA+S+W+ D+ R HR+ + Sbjct: 369 LVNAHDAMKVVREEIFGPVVVAMPYEDLDEVAHRANDTPYGLAASIWSNDLTRVHRLIPK 428 Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 ++ G WVN H +L + MP GG K SG G++M L+ YT + V++ Sbjct: 429 IKAGTVWVNCHNILDNAMPFGGYKQSGIGREMGRAVLDMYTESKSVIM 476 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: 589 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: 478 Length adjustment: 33 Effective length of query: 441 Effective length of database: 445 Effective search space: 196245 Effective search space used: 196245 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 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