Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_010529652.1 ON01_RS03640 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_000224785.1:WP_010529652.1 Length = 392 Score = 372 bits (956), Expect = e-108 Identities = 178/379 (46%), Positives = 250/379 (65%) Query: 6 RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65 ++ LPPYLF+ I++ + +E GVD+I LGIG PD+PTP ++DKL E+ P NHRY Sbjct: 7 KVSNLPPYLFSEIQQMKKKLQEDGVDVIDLGIGAPDLPTPDFIVDKLAEESKIPANHRYS 66 Query: 66 TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125 G FR+AVA +Y++ Y VDLD EV+ +IGSKEGIA++ ++PGD+ LVPDPG Sbjct: 67 AYSGSKEFREAVAHFYKKQYDVDLDTETEVLAVIGSKEGIANLMHATINPGDMVLVPDPG 126 Query: 126 YPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLK 185 YPVY LAGG+S +PL NG+ P + + +AKLM +NYP NPT A A+ Sbjct: 127 YPVYETAVHLAGGKSAALPLDDTNGYAPLYDHVDQESINQAKLMLLNYPGNPTAATANYD 186 Query: 186 FFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGW 245 F + V +R+ L++ +DAAY IT+ GY+APS LQ P AKE+ +EF S+SK +NMTGW Sbjct: 187 TFLKAVALSRANQLLLVNDAAYDMITFKGYKAPSVLQVPDAKELAVEFGSLSKSFNMTGW 246 Query: 246 RLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIV 305 R+G+ G +VI ALA KSNID+ F +Q A AAL + + +YQ+R + + Sbjct: 247 RIGYVVGNREVISALATFKSNIDTSQFLPIQKAAAAALRSDFSAVKKHNTIYQQRMEKLY 306 Query: 306 EGFNSLGWHLEKPKATFYVWAPVPRGYTSASFAEMVLEKAGVIITPGNGYGNYGEGYFRI 365 + F LG +KP T ++WA VP G+TS SFA +L + GVI+TPGN +G+ GEGYFR+ Sbjct: 307 KAFKKLGIKADKPNGTIFLWAKVPDGFTSMSFANKLLHEGGVIVTPGNAFGSRGEGYFRV 366 Query: 366 ALTISKERMQEAIERLRRV 384 ALT++ ER+ + I R+ ++ Sbjct: 367 ALTVTSERLDDVIVRMSQL 385 Lambda K H 0.320 0.139 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: 452 Number of extensions: 15 Number of successful extensions: 1 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: 390 Length of database: 392 Length adjustment: 31 Effective length of query: 359 Effective length of database: 361 Effective search space: 129599 Effective search space used: 129599 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: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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