Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate 8499807 DvMF_0572 Threonine aldolase (RefSeq)
Query= BRENDA::Q88R13 (346 letters) >FitnessBrowser__Miya:8499807 Length = 341 Score = 277 bits (709), Expect = 2e-79 Identities = 152/340 (44%), Positives = 215/340 (63%), Gaps = 5/340 (1%) Query: 6 QQFASDNYSGICPEAWVAMEKANRGHDRAYGDDQWTERASEYFRNLFETDCEVFFAFNGT 65 + FASDN SG+ P AME+AN GH R YG D +TE+A E F F D +++F F GT Sbjct: 4 KSFASDNTSGVHPRILAAMERANAGHARPYGQDPYTEQAKEVFARHFGPDIDMYFVFLGT 63 Query: 66 AANSLALASLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLTAASVNGKLTPQSIREV 125 AAN L L ++ + +HSV+C++ AH+ DECGAPE + GSKL S +G++ + + Sbjct: 64 AANVLGLRAVTRPWHSVVCADVAHINVDECGAPESVT-GSKLQVIPSHDGRIRVMDVVPL 122 Query: 126 ALKRQDIHYPKPRVVTITQATEVGTVYRPDELKAISATCKELGLNLHMDGARFTNACAFL 185 + H+ +PRV++ITQ+TE+GTVY P +++A++ G+ LHMDGAR NA A L Sbjct: 123 LHMIGNFHHSQPRVISITQSTELGTVYSPAQIRALADFAHANGMLLHMDGARLANAAAAL 182 Query: 186 GCSPAELTWKAGVDVLCFGGTKNGMAVGEAILFFNRQLAEDFDYRCKQAGQLASKMRFLS 245 S A LT AGVDVL FGGTKNGM GEA++FFN +L+ +F++ KQ QL SKMRF++ Sbjct: 183 DVSLAALTRDAGVDVLSFGGTKNGMMFGEAVIFFNPELSREFNFIRKQGMQLISKMRFIA 242 Query: 246 APWVGLLEDGAWLRHGNHANHCAQLLASLVSDLPGVELMFPVEANGVFLQM-PEHAIEAL 304 A ++ +L DG WL + +AN A+L+A + LP V + PVEAN VF ++ PEH A Sbjct: 243 AQFMEMLNDGLWLENARNANAMARLMADSLRGLPHVTITRPVEANAVFARLSPEHI--AR 300 Query: 305 RGKGWRFYTFIG-SGGARFMCSWDTEEARVRELAADIRTI 343 + + FY + R+M S+DT E VRE ++ + Sbjct: 301 LQQDFYFYEWDPVLHEVRWMTSFDTTEEDVREFTDAVKAL 340 Lambda K H 0.321 0.134 0.420 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: 286 Number of extensions: 8 Number of successful extensions: 3 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: 346 Length of database: 341 Length adjustment: 29 Effective length of query: 317 Effective length of database: 312 Effective search space: 98904 Effective search space used: 98904 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 (21.9 bits) S2: 49 (23.5 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