Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011766165.1 AZO_RS12285 2-hydroxymuconic semialdehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000061505.1:WP_011766165.1 Length = 484 Score = 304 bits (779), Expect = 4e-87 Identities = 181/481 (37%), Positives = 255/481 (53%), Gaps = 19/481 (3%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAF-AEWGQTTPKVRAE 65 INGE V+ + +P + + EA +VDAAV AA AA WG+ T R + Sbjct: 8 INGEFVA-TAKPFDKCSPLDNRRIALVHEAGKTEVDAAVAAAQAALKGPWGRMTVAERVD 66 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125 L +AD I F E + GKP A + +IP F+ FA + + E Sbjct: 67 LLNAVADGINRRFDDFLAAECADTGKPKSLASHIDIPRGAANFKVFADVIKSV----PTE 122 Query: 126 YLE-------GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITP 178 + E G + R P+GVV I PWN PL++ WK+ PALA GN VV+KPSE TP Sbjct: 123 FFEMATPDGRGALNYALRRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETP 182 Query: 179 LTALKLAELAKDI-FPAGVINILFGRGK-TVGDPLTGHPKVRMVSLTGSIATGEHIISHT 236 TA L E+ ++ P GV N++ G G + G+ +T HPKV ++ TG TG I+ Sbjct: 183 QTATLLGEVMNEVGMPKGVYNVVHGFGPGSAGEFVTTHPKVNAITFTGETRTGAAIMKAA 242 Query: 237 ASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTL 296 A + +E+GGK P IVF D D +A +EG + N GQ C R+Y ++ I+D Sbjct: 243 ADGARPVSLEMGGKNPAIVFADCDFDAAIEGTMRSVFANCGQVCLGTERVYVERPIFDRF 302 Query: 297 VEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-- 354 V L A LK G PDD ST +GPL S H +V +A+ G V GG + Sbjct: 303 VAALKAGAEGLKLGVPDDASTGMGPLISQEHKNKVLSYYNKARELGATVVTGGGVPQMPG 362 Query: 355 --GNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWT 412 NG + PT+ G + I ++E+FGP + PFD E++V+ AND+ YGLA SVWT Sbjct: 363 ELANGAWVQPTIWTGLDDNSPIAREEIFGPCTLIQPFDAEDEVIRRANDTDYGLACSVWT 422 Query: 413 KDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 KD+ RAHRV+ +++ G WVN+ F+ P GG K SG G++ ++ LE YT +++ + Sbjct: 423 KDLARAHRVAGQIEAGLVWVNSWFLRDLRTPFGGAKQSGIGREGGVHSLEFYTEQKNICI 482 Query: 473 K 473 K Sbjct: 483 K 483 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: 562 Number of extensions: 21 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: 484 Length adjustment: 34 Effective length of query: 440 Effective length of database: 450 Effective search space: 198000 Effective search space used: 198000 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