Align ethanolamine utilization protein eutD (characterized)
to candidate WP_046008430.1 OLEAN_RS05710 phosphate acetyltransferase
Query= CharProtDB::CH_024378 (338 letters) >NCBI__GCF_000967895.1:WP_046008430.1 Length = 326 Score = 322 bits (824), Expect = 1e-92 Identities = 163/320 (50%), Positives = 224/320 (70%), Gaps = 2/320 (0%) Query: 2 IIERCRELALRAPARVVFPDALDQRVLKAAQYLHQQGLATPILVANPFELRQFALSHGVA 61 ++++CR ++P R+VF D+LD RVL+AA L +QGLA PIL+ NPFE+R +A +G+A Sbjct: 3 VVQQCRTECKQSPQRIVFADSLDVRVLQAANELQKQGLAEPILIGNPFEIRDYAYRNGIA 62 Query: 62 MDGLQVIDPHGNLAMREEFAHRWLARAGEKTPPDALEKLT-DPLMFAAAMVSAGKADVCI 120 M V+DP + E F + +L + T D+ E L PL +AA MV +ADVCI Sbjct: 63 MPCFAVVDPERS-GYLEPFVNAYLENSDANTERDSAEALLRKPLFYAAMMVKQNQADVCI 121 Query: 121 AGNLSSTANVLRAGLRIIGLQPGCKTLSSIFLMLPQYSGPALGFADCSVVPQPTAAQLAD 180 AGNLS++ +VLRA L++IG+ +T+SS F+M FAD +VVP+PT QLAD Sbjct: 122 AGNLSTSGDVLRAALKVIGIAEQHRTVSSFFVMTSPDGSDVRLFADAAVVPEPTVEQLAD 181 Query: 181 IALASAETWRAITGEEPRVAMLSFSSNGSARHPCVANVQQATEIVRERAPKLVVDGELQF 240 I + +A + +TGE+ RVAMLSFSS GS+ HP +V++A ++VR ++P L+VDGELQF Sbjct: 182 ITIDTARNFEKLTGEKARVAMLSFSSKGSSNHPAAVHVREAFDLVRRKSPDLIVDGELQF 241 Query: 241 DAAFVPEVAAQKAPASPLQGKANVMVFPSLEAGNIGYKIAQRLGGYRAVGPLIQGLAAPM 300 DAA P VA KAP SPL G +NVM+FPSL AGNI YK+AQRL Y+A+GPL+QGL PM Sbjct: 242 DAAVDPIVADHKAPDSPLHGSSNVMIFPSLNAGNIAYKVAQRLAHYQALGPLLQGLRKPM 301 Query: 301 HDLSRGCSVQEIIELALVAA 320 HDLSRGCS +I+++A++A+ Sbjct: 302 HDLSRGCSADDIVDIAILAS 321 Lambda K H 0.320 0.134 0.387 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: 308 Number of extensions: 10 Number of successful extensions: 2 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: 338 Length of database: 326 Length adjustment: 28 Effective length of query: 310 Effective length of database: 298 Effective search space: 92380 Effective search space used: 92380 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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