Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_078716755.1 B5D49_RS06010 LL-diaminopimelate aminotransferase
Query= BRENDA::O66630 (387 letters) >NCBI__GCF_900167125.1:WP_078716755.1 Length = 389 Score = 459 bits (1181), Expect = e-134 Identities = 229/386 (59%), Positives = 281/386 (72%), Gaps = 2/386 (0%) Query: 2 FEFSDRLKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPE 61 F ++R+ LPPYLFA +D+ K E QGVD+I LG+GDPD+PTP+ I++A +A +NP Sbjct: 4 FALAERVASLPPYLFAAIDKAKAEVAAQGVDIISLGIGDPDLPTPEFIIDALYEAAKNPA 63 Query: 62 NHKYPSYVGKYEFRKAVADWYKRRFDVD-LDPNTEVITLIGSKEGIAHFPLAFVNPGDIV 120 NH+YPSY G FR+AVA WY +RFDV+ LDP TEVITLIGSKEGI H P AF+NPGD+ Sbjct: 64 NHQYPSYTGMMRFREAVARWYAQRFDVEGLDPATEVITLIGSKEGIGHLPWAFINPGDLA 123 Query: 121 LCPDPAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNNPTS 180 L P YPVY G FAGG +PL EEN++LPDLD + E+ +AK+I++NYP NPT+ Sbjct: 124 LICPPCYPVYATGVKFAGGEVQELPLLEENDYLPDLDGLDEETWNRAKMIFVNYPGNPTA 183 Query: 181 APPTLEFYKKLVDWAKEYNVIIASDNAYSEIY-TGQEKPPSILQVPGAKDVAIEFHSLSK 239 A T EFY +LV+ AK N I+ SD AYSEIY +KPPSIL VPGAKDVAIEFHSLSK Sbjct: 184 ATATTEFYARLVEKAKATNTIVVSDLAYSEIYYDAAQKPPSILAVPGAKDVAIEFHSLSK 243 Query: 240 TYNMTGWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYR 299 TYNMTGWRI MAVGN++L+ GLGK+K NVDSG F AVQ+AGI AL E VEK R +Y+ Sbjct: 244 TYNMTGWRIAMAVGNEQLINGLGKIKENVDSGAFNAVQEAGIAALEQGEPHVEKARAIYK 303 Query: 300 ERKKIMTEALEKIGLEIYRSDYTFYLWIKVPEGYTSAEFVGRLIDEAGIVCTPGNGFGEY 359 ER+ AL G+E + + ++W +VP TSAEFV L+ + G+V TPG+GFGE Sbjct: 304 ERRDATCAALSAAGIEHRVPEASVFVWARVPGNKTSAEFVTHLLKKTGVVVTPGSGFGEC 363 Query: 360 GEGYFRISLTVPTERLLEAAERIKNL 385 GEGYFRISLTV T+RL EA RI L Sbjct: 364 GEGYFRISLTVDTDRLKEAVSRISQL 389 Lambda K H 0.317 0.139 0.413 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: 482 Number of extensions: 17 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: 387 Length of database: 389 Length adjustment: 30 Effective length of query: 357 Effective length of database: 359 Effective search space: 128163 Effective search space used: 128163 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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