Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate 207344 DVU1878 threonine aldolase, low-specificity
Query= reanno::pseudo3_N2E3:AO353_07670 (346 letters) >MicrobesOnline__882:207344 Length = 340 Score = 285 bits (728), Expect = 2e-81 Identities = 152/339 (44%), Positives = 220/339 (64%), Gaps = 3/339 (0%) Query: 6 QQFASDNYSGICPEAWAAMEQANQGHQRAYGDDEWTARASDDFRKLFETDCEVFFAFNGT 65 + FASDN +G+ P AAM AN+GH +AYG D WT+ A+D FR F D +++F F GT Sbjct: 3 KSFASDNTAGVHPRILAAMASANEGHAKAYGMDPWTSEAADVFRGHFGDDIDLYFVFLGT 62 Query: 66 AANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPESIREI 125 AAN L L S+ + +HSV+C++ AH+ DECGAPE + GSKL + + +G++ I + Sbjct: 63 AANVLGLKSVTRPWHSVVCADVAHINVDECGAPESVT-GSKLQVIPSHDGRIRVMDIVPL 121 Query: 126 ALKRQDIHYPKPRVVTLTQATEVGSIYTPEEIRAISATCKELGLNLHMDGARFSNACAFL 185 + H+ +PRV+++TQ TE+G++Y+P +IRA++ G+ LHMDGAR NA A L Sbjct: 122 MHSLGNFHHSQPRVISITQTTELGTVYSPAQIRALADFAHANGMLLHMDGARLCNAAAAL 181 Query: 186 NCSPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASKMRFLS 245 + A LT GVDVL FGGTKNGM GEA++FFN +LA +F + KQ QL SKMRF++ Sbjct: 182 DTGLAALTRDTGVDVLSFGGTKNGMMFGEAVIFFNRELASEFKFIRKQGMQLVSKMRFIA 241 Query: 246 APWVGLLENDAWLKHARHANYCAQLLAELVSDIPGVELMFPVQANGVFLQLSESAVAALT 305 A ++ LL + WL++AR+AN A+L+AE + +P V + PV+AN VF +LS +AAL Sbjct: 242 AQFIELLRDGLWLENARNANSMARLMAESLRGLPHVTITRPVEANAVFARLSPEHIAAL- 300 Query: 306 AKSWRFYTFIG-KGGARFMCSWDTEVERVRELAADIREV 343 K + FY + R+M S+D+ E+V E I+ + Sbjct: 301 QKDFYFYEWDPVLHEVRWMTSFDSTEEQVMEFVHAIKRL 339 Lambda K H 0.320 0.132 0.408 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: 289 Number of extensions: 7 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: 346 Length of database: 340 Length adjustment: 29 Effective length of query: 317 Effective length of database: 311 Effective search space: 98587 Effective search space used: 98587 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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