Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_003942060.1 C1M55_RS09025 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >NCBI__GCF_002893965.1:WP_003942060.1 Length = 401 Score = 320 bits (819), Expect = 6e-92 Identities = 167/378 (44%), Positives = 242/378 (64%), Gaps = 1/378 (0%) Query: 6 FFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIY 65 F P + V G SL +A + +G R +VTD L G +++ L E+ + + ++ Sbjct: 25 FHAPEI-VFGIGSLVEAAHATLRFGGFRPFLVTDPGLIDAGWVSELEDHLTEQGLTATVW 83 Query: 66 DGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDR 125 G PNP +AAG ++ +E CD +I+LGGGS D AKG+A++AANGG+I DYEGVD+ Sbjct: 84 SGLTPNPKDFEIAAGFEVYQEGECDVIIALGGGSVIDAAKGVAVLAANGGNILDYEGVDQ 143 Query: 126 SAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPK 185 + KP P++ + TT+GT +++++FCI+TD R K+ I+ + + P ++V D L+ MP+ Sbjct: 144 ATKPIPPLVMVPTTSGTGADVSQFCIVTDTTRGTKITIIGRALVPDVTVIDPRLLTTMPE 203 Query: 186 SLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAY 245 L AATG+DALTH IEA+VS+A P+TD AL+AV ++ ENL ++D +AR MA Sbjct: 204 WLNAATGLDALTHGIEAFVSLAHNPLTDHHALRAVGLVTENLVHTIQDPMEMEARSVMAQ 263 Query: 246 AQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAA 305 A AG+AF NA LG HAM+HQ+GG +LPHGV N +LLPHV FNS AA AA Sbjct: 264 ASLEAGLAFTNAILGAAHAMSHQVGGMLDLPHGVINGILLPHVIRFNSTTDAAPFVAIAA 323 Query: 306 AMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFT 365 A+ + E A A + + LA++V +P GL +L V+EED + LA+ AL DAC T Sbjct: 324 ALSLPEQRGTPEEAALAVADRVERLAREVGVPKGLGELGVREEDLSRLASFALLDACMST 383 Query: 366 NPIQATHEEIVAIYRAAM 383 NP +AT E++VA++R A+ Sbjct: 384 NPREATQEQMVALFRGAL 401 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: 401 Number of extensions: 20 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: 401 Length adjustment: 31 Effective length of query: 352 Effective length of database: 370 Effective search space: 130240 Effective search space used: 130240 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 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