Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase
Query= curated2:Q30ZX9 (388 letters) >FitnessBrowser__Smeli:SMc01578 Length = 400 Score = 174 bits (441), Expect = 4e-48 Identities = 120/395 (30%), Positives = 191/395 (48%), Gaps = 21/395 (5%) Query: 6 LADRLATLPPYLFAQIDKVKAEVAARGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANH 65 LAD L+ + P + + E+ A+G D+I LG G+PD TPD + +A A ++ Sbjct: 4 LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDR-GET 62 Query: 66 QYPSYTGMLAFRQEVANWYKRRYAVELDPKTEVLTLIGS--KEGIAHFPTAFVNPGDLVL 123 +Y +G+ R+ +A +KR ++ T T++G+ K+ + + A +NPGD V+ Sbjct: 63 KYTPVSGIPELREAIAKKFKRENNLDY---TAAQTIVGTGGKQILFNAFMATLNPGDEVV 119 Query: 124 VCPPCYPVYAIASRFMGGVVQELPLLEENDFLPDLDAVDEATWEKARCIFVNYPNNPTAA 183 + P + Y GG +P +EN+F + +D A K + N P+NP+ A Sbjct: 120 IPAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGA 179 Query: 184 MAPRSFFEKLIGIARKH-NVIVVHDAAYTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSK 242 + L + KH +V V+ D Y + Y + + PG + + N +SK Sbjct: 180 AYSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSK 239 Query: 243 PYNMTGWRIAMAVGNASLVAGLGKVKENMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYR 302 Y MTGWRI A G L+ + ++ SGA Q AA+ AL F+ ++I++ Sbjct: 240 AYAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQ 299 Query: 303 KRRDTVIAALNKI-GITCRVPEASLYVW--------ARVPEG---YTSSDFVTRVLQETG 350 RRD V++ LN+ GI+C PE + YV+ P G T DFV+ +L+ G Sbjct: 300 GRRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEG 359 Query: 351 VVMTPGNGFGAAGEGYFRISLTVNDERLEEAVSRI 385 V + G+ FG FRIS ++ LEEA RI Sbjct: 360 VAVVHGSAFGLGPN--FRISYATSEALLEEACRRI 392 Lambda K H 0.320 0.136 0.403 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: 382 Number of extensions: 25 Number of successful extensions: 6 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: 388 Length of database: 400 Length adjustment: 31 Effective length of query: 357 Effective length of database: 369 Effective search space: 131733 Effective search space used: 131733 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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