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 PP_2214 PP_2214 3-hydroxyacyl-CoA dehydrogenase type-2
Query= BRENDA::Q99714 (261 letters) >FitnessBrowser__Putida:PP_2214 Length = 255 Score = 253 bits (647), Expect = 2e-72 Identities = 133/246 (54%), Positives = 175/246 (71%), Gaps = 2/246 (0%) Query: 14 VITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQT 73 +++G ASGLG ATA+ LV GA +L+DL EA+A++LG+N FA AD++ E+ Q+ Sbjct: 9 IVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADISDEQAAQS 68 Query: 74 ALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVA 133 A+ A FG + VNCAGI A K L K H L F +V++VNL+G+FN++RL A Sbjct: 69 AVDAAVSAFGSLHGLVNCAGIVGAEKV--LGKQGPHGLASFAKVINVNLIGSFNLLRLAA 126 Query: 134 GEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRV 193 M + D+ G+RGVIINTAS+AA++GQ+GQAAY+ASKG I +TLP AR+LA GIRV Sbjct: 127 AAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIRV 186 Query: 194 MTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIRL 253 MTIAPG+F TP++ + ++V LA+ VPFP RLG P EYA L + IIEN LNGEVIRL Sbjct: 187 MTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSMLNGEVIRL 246 Query: 254 DGAIRM 259 DGA+RM Sbjct: 247 DGALRM 252 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: 199 Number of extensions: 3 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: 255 Length adjustment: 24 Effective length of query: 237 Effective length of database: 231 Effective search space: 54747 Effective search space used: 54747 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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