Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000021485.1:WP_012607209.1 Length = 506 Score = 303 bits (777), Expect = 7e-87 Identities = 173/471 (36%), Positives = 264/471 (56%), Gaps = 15/471 (3%) Query: 15 EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVI 74 +G+ V P G + A ++AE ++ A+ AA A +WG+T+P RA LLK+AD I Sbjct: 32 KGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERANILLKVADRI 91 Query: 75 EENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI 134 E N ++ A E+ + GKP+ N +IP VD FR+FAG R G + E + Sbjct: 92 EANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEG-GISDIDENTVAYH 150 Query: 135 RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPA 194 +PLGVV I PWN+P++MA+WKLAPAL AGN VVLKP+E TP++ L LAEL D+ P Sbjct: 151 FHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPISILILAELIADLLPP 210 Query: 195 GVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVI 254 GV+NI+ G G+ G PL ++ ++ TGS TG I A+S+ +ELGGK+P I Sbjct: 211 GVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANSLIPATLELGGKSPNI 270 Query: 255 VF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLK 308 F DD+ ++ +EG+ F +N G+ CT R Q+ IYD +E+ + +K Sbjct: 271 FFADVMDKDDSFLDKAIEGLVLFA-FNQGEVCTCPSRALIQESIYDKFMERCLDRIKAIK 329 Query: 309 SGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR-----KGNGYYYAPT 363 G P D +T +G +S L ++ ++ K G +V+ GG + GYY PT Sbjct: 330 QGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEG-AQVLIGGSQAIVDGDLDGGYYVQPT 388 Query: 364 LLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSA 423 L G I Q+E+FGPV++VT F +E + ++ AND+ YGL + VW+++ A+R+ Sbjct: 389 LFKGH-NKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAGVWSRNGNVAYRMGR 447 Query: 424 RLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 ++ G W+N + + GG K SG G++ L+ Y ++++V + Sbjct: 448 AIKAGRVWINCYHAYPAHAAFGGYKESGIGRETHKVMLDHYQQTKNLLVSY 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: 558 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: 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