Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_035241269.1 Q366_RS17050 NADP-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000745975.1:WP_035241269.1 Length = 485 Score = 314 bits (805), Expect = 4e-90 Identities = 174/466 (37%), Positives = 268/466 (57%), Gaps = 4/466 (0%) Query: 7 INGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65 I + + + +K V NPATG+VL + A++ A+ AA+ + W T R+ Sbjct: 16 IQDQWIEADSKKNVAVTNPATGEVLGTVPFCGADETRRAIDAANGSLPAWRSKTAAQRSA 75 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125 L + D++ EN + A L + GKPL + EI F +FA A+ + G + Sbjct: 76 ILRRWHDLLMENQEDLALLMTAEQGKPLAES-RGEIAYAASFFEWFAEEAKRIYGDIIPQ 134 Query: 126 YLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185 + ++ + P+GVVA+I PWN+P M K ALAAG +V+KP+ TP +AL +A Sbjct: 135 TIASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVVKPATATPFSALAIA 194 Query: 186 ELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244 +LA++ P GV N++ G +G LT +P VR ++ TGS G+ ++ A ++KR Sbjct: 195 KLAQEAGMPPGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTEVGKKLMQDCAGTMKRVS 254 Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304 MELGG AP IVFDDAD++A VEG + Y N+GQ C A R+Y Q G+YD EKL AV Sbjct: 255 MELGGNAPFIVFDDADLDAAVEGALSCKYRNSGQTCVCANRLYVQAGVYDQFCEKLARAV 314 Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364 ATLK G +E GPL + +E V + + +A G KV+ GG++ G +++PT+ Sbjct: 315 ATLKVGNGIEEGVVQGPLIDMKAVESVERHINDALDKG-AKVLAGGKRHALGGTFFSPTV 373 Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424 LA D + ++E+FGP + F++E +VV AND++YGLA+ +T+D+ R RV + Sbjct: 374 LADVTDDMLVAKEEIFGPFAPIFKFESEAEVVQKANDTEYGLAAYFFTRDMARTWRVGEK 433 Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 L+YG +N+ + + P GG K SG G++ S YGL+DY ++++ Sbjct: 434 LEYGLIGINSGIISNAVAPFGGVKESGNGREGSKYGLDDYLEIKYM 479 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: 514 Number of extensions: 14 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: 485 Length adjustment: 34 Effective length of query: 440 Effective length of database: 451 Effective search space: 198440 Effective search space used: 198440 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 Apr 09 2024. 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