Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_084207246.1 SUTH_RS04155 heavy metal translocating P-type ATPase metal-binding domain-containing protein
Query= BRENDA::Q99714 (261 letters) >NCBI__GCF_000828635.1:WP_084207246.1 Length = 1079 Score = 266 bits (679), Expect = 2e-75 Identities = 137/249 (55%), Positives = 174/249 (69%), Gaps = 2/249 (0%) Query: 8 VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTS 67 +K V ++TGGASGLG TA LV QG V+ DL + G+A +LG N F +V Sbjct: 3 IKDSVFIVTGGASGLGAGTARMLVAQGGKVVMADLNEAAGKALEAELGGNARFVATNVAD 62 Query: 68 EKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFN 127 E + +A A+ FG + VNCAGIA A K L K H L+ F + + VNL+G+FN Sbjct: 63 EASARACVAAAQAAFGGLHGLVNCAGIATAEKV--LGKNGPHALDTFAKTITVNLVGSFN 120 Query: 128 VIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187 +IRL + M Q P+ G+RGVI++TASVAA++GQ+GQAAY+ASKGG+VGMTLPIAR+LA Sbjct: 121 MIRLASEVMSQGAPNAAGERGVIVSTASVAAYDGQIGQAAYAASKGGVVGMTLPIARELA 180 Query: 188 PIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLN 247 GIRVMTIAPG+F TP+L +P++V + L VPFPSRLG PAEYA LV+ I+EN LN Sbjct: 181 RFGIRVMTIAPGIFETPMLLGMPQEVQDALGKMVPFPSRLGKPAEYAALVRHIVENEMLN 240 Query: 248 GEVIRLDGA 256 GEVIRLDGA Sbjct: 241 GEVIRLDGA 249 Lambda K H 0.318 0.135 0.385 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: 646 Number of extensions: 24 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: 261 Length of database: 1079 Length adjustment: 35 Effective length of query: 226 Effective length of database: 1044 Effective search space: 235944 Effective search space used: 235944 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