Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_025367279.1 THITH_RS04650 alanine transaminase
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_000227685.2:WP_025367279.1 Length = 410 Score = 375 bits (964), Expect = e-109 Identities = 174/380 (45%), Positives = 251/380 (66%), Gaps = 3/380 (0%) Query: 6 RIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYP 65 RI LPPY+F + + AEAR RG DII G+G+PD PTP H++DKLV A + HRY Sbjct: 7 RIERLPPYVFNIVNQLKAEARARGEDIIDFGMGNPDQPTPQHIVDKLVEVAQRGDTHRYS 66 Query: 66 TSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPG 125 S+G+ R+A+ WY+ Y VDLDP E + IGSKEG+AH++L + PGD LVP+P Sbjct: 67 VSKGIPRLRRAITRWYKAHYDVDLDPETEAIVTIGSKEGLAHLALATLGPGDAVLVPNPA 126 Query: 126 YPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLK 185 YP++ G ++AG + +PLT F +L D R K++ +N+P NPT DL Sbjct: 127 YPIHPYGCVIAGADVRHVPLTPNVDFFAELHRAIQDSWPRPKMLILNFPANPTTQCVDLD 186 Query: 186 FFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYNMTGW 245 FF+ VV+ R + + HD AY+EI +DGY+APS LQ PGAKE+ +EF ++SK YNM GW Sbjct: 187 FFERVVKICREQHIWLVHDLAYAEIVFDGYKAPSVLQVPGAKEIAVEFYTLSKTYNMPGW 246 Query: 246 RLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIV 305 R+G+ CG ++ ALAR+KS +D G F +Q A IAAL GPQ+ + E+ Y+ RRD++ Sbjct: 247 RIGFMCGNPTLVAALARMKSYLDYGTFTPIQVAAIAALEGPQDCVQEICETYRARRDVLC 306 Query: 306 EGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGNYGEGY 362 +G N++GW +EKPKAT +VWAP+P GY S F++ +L A V ++PG G+GNYG+ + Sbjct: 307 DGLNAIGWQVEKPKATMFVWAPIPPGYREMGSLEFSKKLLRDAKVAVSPGIGFGNYGDSH 366 Query: 363 FRIALTISKERMQEAIERLR 382 R +L +++R ++A+ ++ Sbjct: 367 VRFSLIENEQRTRQALRGIK 386 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: 483 Number of extensions: 25 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: 410 Length adjustment: 31 Effective length of query: 359 Effective length of database: 379 Effective search space: 136061 Effective search space used: 136061 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 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