Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate Echvi_0146 Echvi_0146 Nucleoside-diphosphate-sugar epimerases
Query= reanno::Cup4G11:RR42_RS28300 (324 letters) >FitnessBrowser__Cola:Echvi_0146 Length = 325 Score = 373 bits (958), Expect = e-108 Identities = 176/307 (57%), Positives = 223/307 (72%), Gaps = 2/307 (0%) Query: 7 VLIIGANGQLGTELASALADRYGKQNVVTSDMVPHGRHL--HLTHEMLDVTDRAHLRDVI 64 +LI GA GQLG+EL ALA+ YG ++ +D+ + + LDV DR + +++ Sbjct: 11 ILITGAAGQLGSELTLALANMYGGDRIIATDINEASAYKFDYCRFMALDVMDRKRMTEIV 70 Query: 65 ERHGITQIYHLAAALSATGEKSPTWAWQLNMNGLLNVLEAARHQKLDKVFWPSSIAAFGP 124 + +TQIYHLAA LSAT EK+P +AW LNM LL++LE AR QKL+K++WPSSIA FGP Sbjct: 71 KAEKVTQIYHLAAILSATSEKNPIFAWNLNMESLLSILEIAREQKLNKIYWPSSIAVFGP 130 Query: 125 TTPPDGTPQSTIMEPKTVYGISKLAGEGWCRWYFENHGVDVRSLRYPGLISYKTPPGGGT 184 TP TPQ IM+P TVYGISK AGE WC +YFE GVDVRSLRYPGLI YK+ PGGGT Sbjct: 131 NTPMQHTPQDCIMDPNTVYGISKQAGERWCAYYFEKFGVDVRSLRYPGLIGYKSMPGGGT 190 Query: 185 TDYAIDIFHSALRAQPYACFLEKDEALPMMYMPDAVRATMELMEAPRASISERGSYNLAG 244 TDYA+DIFH A+ + + CFLE+D LPMMYM DA++AT++LM AP A I R SYNL G Sbjct: 191 TDYAVDIFHKAIEGEDFECFLEEDTYLPMMYMDDAIKATLDLMHAPAAQIKVRSSYNLGG 250 Query: 245 LSFTPGEIANEIRRHCPGFDVRYEPDFRQEIAAGWPDSIDDSVARRDWNWRPEFGLKEMV 304 +SF+P EI I++H P F++ Y+PDFRQ+IA WPDSIDDS A+ DW W+ +GL+EM Sbjct: 251 ISFSPKEIYECIKQHYPNFNITYKPDFRQQIADTWPDSIDDSAAQNDWGWQHSYGLEEMT 310 Query: 305 ADMLKNL 311 D+L NL Sbjct: 311 KDILANL 317 Lambda K H 0.319 0.135 0.421 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: 341 Number of extensions: 9 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: 324 Length of database: 325 Length adjustment: 28 Effective length of query: 296 Effective length of database: 297 Effective search space: 87912 Effective search space used: 87912 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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