Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_106714455.1 CU102_RS29015 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >NCBI__GCF_003010955.1:WP_106714455.1 Length = 388 Score = 199 bits (507), Expect = 8e-56 Identities = 120/381 (31%), Positives = 195/381 (51%), Gaps = 11/381 (2%) Query: 9 PSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGT 68 P+ GA + + ++ G + L VTD L KL + K L++ + ++ Sbjct: 11 PTTVRFGAGRIKELPEVLEATGIKKPLFVTDPGLAKLPVVASTLKILDDAKVPYGVFSDV 70 Query: 69 QPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD---- 124 +PNP N+ AG+ + K+ D VI+ GGGS D K IA A + D+E V Sbjct: 71 KPNPVDSNLTAGIAVFKKGKHDGVIAFGGGSALDLGKLIAFQAGQTRPVWDFEDVGDWWK 130 Query: 125 -RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183 ++ P+IA+ TTAGT SE+ R +IT+E H K I + P + + D L +GM Sbjct: 131 RANSNAIAPIIAVPTTAGTGSEVGRAGVITNEETHTKKVIFHPKLLPAVVIADPELSVGM 190 Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243 P +TA TGMDAL H +EAY + P+ D A++ + ++ ENLP A +G + AR M Sbjct: 191 PAFITAGTGMDALAHCLEAYCAPGYHPMADGIAVEGIRLVFENLPKAYANGKDLTARAHM 250 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303 A + AF LG +H+++H +G Y+ HG+ NAV +P+V FN + R+ Sbjct: 251 MSAATMGAAAFQK-GLGAIHSLSHPIGALYDTHHGMTNAVFMPYVLAFNREAVDERIARL 309 Query: 304 AAAMGVNVTGKNDAEG-AEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDAC 362 A+ +G+ K G A+A I +EL +P ++DL++ ++ ++A A+ D Sbjct: 310 ASYIGI----KGGFNGFAKAVIKLRKELKVPHTLPGLIKDLDMTKKQKELIADMAIVDPT 365 Query: 363 GFTNPIQATHEEIVAIYRAAM 383 NP++ T + + + A+ Sbjct: 366 AGGNPVKLTKKAALKLLDEAI 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: 362 Number of extensions: 20 Number of successful extensions: 4 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: 388 Length adjustment: 30 Effective length of query: 353 Effective length of database: 358 Effective search space: 126374 Effective search space used: 126374 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