Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000021485.1:WP_012536996.1 Length = 506 Score = 304 bits (779), Expect = 4e-87 Identities = 175/470 (37%), Positives = 260/470 (55%), Gaps = 15/470 (3%) Query: 16 GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75 GE +P G +I +SAE ++ A+ AA AA WG+T+ R+ LLK+AD I+ Sbjct: 33 GEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAAKDAWGRTSVTARSNILLKIADRID 92 Query: 76 ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIR 135 N ++ A E+ + GK + N ++P D FR+FAG R G GE E + Sbjct: 93 ANLEMLAVAETWDNGKAVRETLNADVPLSSDHFRYFAGCLRAQEG-TIGEIDENTVAYHF 151 Query: 136 RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAG 195 +PLGVV I PWN+PL+MA WKLAPALAAGNCVVLKP+E TP + L + EL D+ PAG Sbjct: 152 HEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASILVMMELIADLLPAG 211 Query: 196 VINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIV 255 V+N++ G G G L ++ ++ TGS G I+ + A +I + +ELGGK+P I Sbjct: 212 VLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMKYAAENIIPSTVELGGKSPNIF 271 Query: 256 F------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKS 309 F +DA + VEG ++N G+ CT R+ Q+ IY+ + + A +K Sbjct: 272 FADVLDQEDAFVSKAVEGA-VLAFFNQGEVCTCPSRLLIQESIYEKFIGMVVERSAQIKR 330 Query: 310 GAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGN-----GYYYAPTL 364 G P D +G +S +++ ++ K G +VITGG + GYY PTL Sbjct: 331 GNPLDTEVMVGAQASQEQYDKILSYIQIGKDEG-AEVITGGAVETMSADYCEGYYIQPTL 389 Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424 L G + + Q+E+FGPVVSVT F +E + + AND ++GL + VWT+D+ RA+R+ Sbjct: 390 LKGT-NNMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLGAGVWTRDMNRAYRMGRG 448 Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 +Q G W N + M + GG K SG G++ L+ Y ++++V + Sbjct: 449 IQAGRVWTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNLLVSY 498 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: 571 Number of extensions: 23 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: 506 Length adjustment: 34 Effective length of query: 440 Effective length of database: 472 Effective search space: 207680 Effective search space used: 207680 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