Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 6938336 Sama_2455 alcohol dehydrogenase II (RefSeq)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__SB2B:6938336 Length = 382 Score = 526 bits (1354), Expect = e-154 Identities = 263/381 (69%), Positives = 312/381 (81%) Query: 3 ASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFS 62 A+ FFIPSVNV+G ++ +A+ + GF + LIVTD L ++G+AG++ + L ER I + Sbjct: 2 AAKFFIPSVNVLGQGAVDEAIGDIVTLGFKQALIVTDKPLVQIGIAGELVEKLGERGITA 61 Query: 63 VIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEG 122 V++DG QPNPTT NV AGL LL + CD VISLGGGSPHDCAKGIALVA NGG I+DYEG Sbjct: 62 VVFDGVQPNPTTANVEAGLALLNAHGCDFVISLGGGSPHDCAKGIALVATNGGSIKDYEG 121 Query: 123 VDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIG 182 VD+SAKPQLP++AINTTAGTASEMTRFCIITDEARHIKMAIVDKH TP+LSVND LM+ Sbjct: 122 VDKSAKPQLPLVAINTTAGTASEMTRFCIITDEARHIKMAIVDKHTTPILSVNDPELMVK 181 Query: 183 MPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREA 242 P +LTAATGMDALTHA+EAYVS+AA PITDACA+KA+ +I + L AV+ G + +ARE Sbjct: 182 KPAALTAATGMDALTHAVEAYVSVAANPITDACAIKAIELIQQYLERAVKQGQDLQAREQ 241 Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRD 302 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFY+LPHGVCNA+LLP+VQ +N+ VAAARL+D Sbjct: 242 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYDLPHGVCNALLLPYVQEYNAAVAAARLKD 301 Query: 303 CAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDAC 362 A AMGV V G +D EGA+A I+AI+ L+K V+IP L L VKEED +LA NALKDAC Sbjct: 302 VAKAMGVAVDGLDDQEGAKAAISAIKALSKAVNIPENLTVLGVKEEDIPLLADNALKDAC 361 Query: 363 GFTNPIQATHEEIVAIYRAAM 383 GFTNP QATHEEI I+ A+ Sbjct: 362 GFTNPKQATHEEICQIFCNAL 382 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: 521 Number of extensions: 16 Number of successful extensions: 1 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: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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 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