Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 254 bits (648), Expect = 6e-72 Identities = 155/475 (32%), Positives = 250/475 (52%), Gaps = 11/475 (2%) Query: 7 INGELVSGEGEKQ-PVYNPAT-GDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRA 64 ING+ ++ E +NPA +++ + A+ D AV AA A+ W + RA Sbjct: 11 INGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAPARA 70 Query: 65 ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124 E + ++ +++ ++ + A+L SR GKP+ A D + VD + AG R L G Sbjct: 71 EYIFRVGELLLQHKEELAQLISREMGKPITEARGD-VQEGVDCAFYSAGEGRRLFGQTTP 129 Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184 + +M R P+GV A I PWN+P+ + WK PAL GN V+LKP+E TP A KL Sbjct: 130 SEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACATKL 189 Query: 185 AEL-AKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRT 243 E+ A P GVIN++ G G+ G L HP + +VS TGS ATG ++ + KR Sbjct: 190 IEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTHKRV 249 Query: 244 HMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAA 303 +E+GGK +V +DAD+E ++G + GQ CTA R+ + I + L Sbjct: 250 CLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTMLRER 309 Query: 304 VATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG----EKRKGNGYY 359 + L+ GA + T++GP+ + L+RV + + A+ G K++ GG E + GY+ Sbjct: 310 TSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEG-AKILIGGEIVTEGQLKQGYF 368 Query: 360 YAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAH 419 + PT+L + ++E+FGPVV++ E+ + ND++YGL+SSV+T+D+ RA Sbjct: 369 FQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINRAF 428 Query: 420 RVSARLQYGCTWVNTHFMLVS-EMPHGGQKLSGYG-KDMSLYGLEDYTVVRHVMV 472 ++ G T++N + +P GG K +G G ++ L+ +T + V V Sbjct: 429 VAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKSVYV 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: 548 Number of extensions: 31 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: 498 Length adjustment: 34 Effective length of query: 440 Effective length of database: 464 Effective search space: 204160 Effective search space used: 204160 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: 52 (24.6 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