Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_010532097.1 ON01_RS16395 aldehyde dehydrogenase family protein
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000224785.1:WP_010532097.1 Length = 506 Score = 302 bits (774), Expect = 2e-86 Identities = 171/462 (37%), Positives = 259/462 (56%), Gaps = 13/462 (2%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 +P TG V E+A ++ E V+AAV A AA W QT+ RA+ L K+AD +EEN + A Sbjct: 40 SPVTGKVFCELARSTKEDVEAAVDAGYAAKDAWAQTSVAERADILNKIADRMEENLESLA 99 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVV 142 E+ + GK + +IP VD FR+FAGA R G + + +PLGVV Sbjct: 100 VAETWDNGKAVREGLAADIPLAVDHFRYFAGAIRAQEG-GVSQIDNDTVAYHFHEPLGVV 158 Query: 143 ASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFG 202 I PWN+P++MA WKLAPALAAGNCVVLKP+E TP + L +L KD+ PAGV+NI+ G Sbjct: 159 GQIIPWNFPILMATWKLAPALAAGNCVVLKPAEQTPASIHVLLDLIKDLLPAGVLNIVNG 218 Query: 203 RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF------ 256 G G PL + ++ ++ TG TG I+ + + +I +ELGGK+P I F Sbjct: 219 FGVEAGKPLASNSRISKIAFTGETTTGRLIMQYASENIIPVTLELGGKSPNIFFPDVMDK 278 Query: 257 DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316 DD ++ +EG+ F N G+ CT R + IYD +E+ V +K G P D Sbjct: 279 DDGFLDKAIEGLVMFA-LNQGEVCTCPSRALVHESIYDEFMERAIKRVNEIKIGHPLDTD 337 Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGG-EKRKGN---GYYYAPTLLAGALQDD 372 T +G +SL +E++ ++ + G ++ GG + KG+ GYY PT+ G Sbjct: 338 TMMGAQASLEQMEKIKSYLDIGRQEGAEVLVGGGVNQLKGDMEEGYYIEPTIFKGD-NKM 396 Query: 373 AIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWV 432 I Q+E+FGPV++VT F+ ++ + AND+ YGL + VWT+++ A+R ++ G W+ Sbjct: 397 RIFQEEIFGPVLAVTTFNENDEAMKIANDTLYGLGAGVWTRNINTAYRFGRGIEAGRVWM 456 Query: 433 NTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 N + + GG K SG G++ L L+ Y +++++ + Sbjct: 457 NCYHQYPAHAAFGGYKKSGIGRENHLMMLDHYQQTKNLLISY 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: 600 Number of extensions: 26 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 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