Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate WP_077278775.1 B1C78_RS08600 alanine transaminase
Query= SwissProt::Q2RK33 (390 letters) >NCBI__GCF_002000365.1:WP_077278775.1 Length = 399 Score = 375 bits (962), Expect = e-108 Identities = 175/385 (45%), Positives = 253/385 (65%), Gaps = 3/385 (0%) Query: 1 MQEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPE 60 + E RI+ LPPY+F + A+AR RG DII G+G+PD PTP H++DKL A + Sbjct: 2 IDEFPRIKRLPPYVFNIVNDLKAKARARGEDIIDFGMGNPDQPTPKHIVDKLCEVAQRDD 61 Query: 61 NHRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINL 120 HRY S G+ R+A+ WY+ + VDLDP E + IGSKEG+AH++L + PGD L Sbjct: 62 THRYSMSRGIPRLRRAITRWYKDRFNVDLDPETEAIVTIGSKEGLAHLALATLGPGDAVL 121 Query: 121 VPDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGA 180 VP+P YP++ G ++AG + +PLT F +L D R K++ +++P NPT Sbjct: 122 VPNPAYPIHPYGCVIAGADIRHVPLTPGVDFFAELEKAIQDSWPRPKMLVLSFPANPTAQ 181 Query: 181 VADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPY 240 +L FF++V++ AR Y + V HD AY+EIT+DGYRAPS LQ GAK+V +EF S+SK Y Sbjct: 182 CVELGFFEKVIDIAREYGIWVVHDLAYAEITFDGYRAPSILQVSGAKDVAVEFYSLSKSY 241 Query: 241 NMTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQER 300 NM GWR+G+ CG ++ AL RIKS +D G F +Q A IAAL GPQ+ + ++R++YQ R Sbjct: 242 NMPGWRVGFMCGNPKLVAALGRIKSYLDYGTFTPIQVASIAALEGPQDCVGQIRQLYQSR 301 Query: 301 RDIIVEGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGN 357 RD++ +G N+LGW +EKPKAT +VWAP+P Y S F++ +L+ A V +PG G+G+ Sbjct: 302 RDVLCDGLNALGWVVEKPKATMFVWAPIPEQYVHMGSLEFSKKLLKDAKVAASPGVGFGS 361 Query: 358 YGEGYFRIALTISKERMQEAIERLR 382 YG+ Y R L ++ R ++A+ ++ Sbjct: 362 YGDQYVRFGLIENEHRTRQAVRGIK 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: 466 Number of extensions: 20 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: 399 Length adjustment: 31 Effective length of query: 359 Effective length of database: 368 Effective search space: 132112 Effective search space used: 132112 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