Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate Echvi_0924 Echvi_0924 Alcohol dehydrogenase, class IV
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Cola:Echvi_0924 Length = 381 Score = 183 bits (464), Expect = 8e-51 Identities = 109/317 (34%), Positives = 167/317 (52%), Gaps = 4/317 (1%) Query: 64 IYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGV 123 +YD +P T + LK +K+ D+++ +GGGS D AK +A + + G + D+ G+ Sbjct: 64 VYDAGEP--TFSHYEDFLKQVKDFGADTIVGIGGGSVLDLAKLLAAMQDSTGQLSDFVGI 121 Query: 124 DRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183 + M+ I TTAGT SE++ I+ DEA K I+ + P + D +L +G+ Sbjct: 122 NLLESRNTHMVCIPTTAGTGSEVSPNAILLDEATLEKKGIISPFLVPDATYIDPALTVGL 181 Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243 P +TA TG+DAL+H IEAY + + P+ D AL+ + +I +NL A E + AR A+ Sbjct: 182 PPKITAETGIDALSHCIEAYTNKFSHPLVDDYALRGIALIGQNLHRAFEVPEDMDARTAV 241 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303 A G+ + VHA+++ LGG Y++PHG+ NAVLLP V +N + Sbjct: 242 ALGSMYGGLCLGPVNTAAVHALSYPLGGKYHVPHGLANAVLLPEVMAYNLSSNIQKHEQI 301 Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALK-DAC 362 A AMG G + E A + ++EL K+ DIP L L V++ED L A+K Sbjct: 302 ALAMGAE-QGNSPEETASNGVQKVKELVKRCDIPQDLTTLGVQQEDVPELTALAMKVTRL 360 Query: 363 GFTNPIQATHEEIVAIY 379 NP + T + IY Sbjct: 361 LKNNPREVTFADAEEIY 377 Lambda K H 0.318 0.131 0.373 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: 312 Number of extensions: 12 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: 383 Length of database: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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 (21.8 bits) S2: 50 (23.9 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