Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 208042 DVU2545 alcohol dehydrogenase, iron-containing
Query= ecocyc::EG12293-MONOMER (383 letters) >MicrobesOnline__882:208042 Length = 386 Score = 270 bits (690), Expect = 5e-77 Identities = 154/377 (40%), Positives = 214/377 (56%) Query: 7 FIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYD 66 F+ V G + A + + G TR L+VTD + + G A V +L I ++ Sbjct: 10 FVAPEFVFGNGAARLAGRYVHNLGGTRCLVVTDPGVMRNGHADTVIGSLTAYGIAHAVFQ 69 Query: 67 GTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRS 126 PNP V G++ CD+++++GGGSP DCAKGI +VA+NGG I YEGVD Sbjct: 70 DISPNPRDVEVQRGVEAYHREGCDAIVAVGGGSPIDCAKGIGIVASNGGSISLYEGVDAI 129 Query: 127 AKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKS 186 KP P++ + TTAG+A+++++F IITD R +K+AIV K +S+ D S M + Sbjct: 130 PKPMPPLVCVPTTAGSAADVSQFAIITDTTRMVKIAIVSKAAVADVSLIDPSTTKSMSRD 189 Query: 187 LTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYA 246 LTAATG+D LTHAIEA+ S A+ PITD AL+A++++ +LP + DG + ARE MA A Sbjct: 190 LTAATGIDTLTHAIEAFASNASGPITDMFALEAISLVNTHLPQVLADGDDDTAREGMALA 249 Query: 247 QFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAA 306 AG+AF+NA LG VHAMAH LGG +LPHG CNA+LLP V N A R A A Sbjct: 250 CLNAGLAFSNAILGAVHAMAHSLGGLLDLPHGECNAILLPFVVRRNFDAAPVRYARVANA 309 Query: 307 MGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTN 366 +G++V G +A + + L GL V E LA A++D C TN Sbjct: 310 LGIDVGGTPATAIRDALFDRLMTLRTAAGFTRGLSAFGVTREQIGRLARLAVEDPCLATN 369 Query: 367 PIQATHEEIVAIYRAAM 383 P +I ++Y A+ Sbjct: 370 PEALDIADIESLYAEAL 386 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: 396 Number of extensions: 13 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: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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