Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 8499593 DvMF_0361 LL-diaminopimelate aminotransferase (RefSeq)
Query= BRENDA::Q02635 (400 letters) >FitnessBrowser__Miya:8499593 Length = 389 Score = 172 bits (436), Expect = 2e-47 Identities = 117/393 (29%), Positives = 186/393 (47%), Gaps = 16/393 (4%) Query: 4 LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDR-GET 62 LAD L+ + P + + E+ A+G D+I LG G+PD TPD I +A A++R Sbjct: 6 LADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMPTPDFIIEAMKKAVERPANH 65 Query: 63 KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGT-GGKQILFNAFMATLNPGDEVVIP 121 +Y G+ E R+ +A + R + ++G G K+ + + +A +NPGD V++ Sbjct: 66 QYPSYVGMLEFRQEVANWYGRRFGVSLDPKTEVIGLIGSKEGIAHFPLAFVNPGDLVLVC 125 Query: 122 APYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAY 181 P + Y GG F+P +EN++ + + A + K N P+NP+ A Sbjct: 126 TPNYPVYHIATGFVGGEVQFIPLVEENDYLPDLDAIPAATWDRAKMIFVNYPNNPTAATA 185 Query: 182 SHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAY 241 + L + KH +V + D Y + Y + + G + T+ + +SK Y Sbjct: 186 PRAFYEKLIGICRKH-NVIIAHDTAYTEVYYDENDKPMSILEVEGAKDVTIEFHSLSKTY 244 Query: 242 AMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGR 301 MTGWR+G A G L+ + ++ SG Q A++ AL DF + I++ R Sbjct: 245 NMTGWRVGMAVGNASLVAGLGKVKENVDSGIFQAVQEASIVALRDGDDFCRELRGIYRKR 304 Query: 302 RDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVA 361 RD+VV+ LN+ GI+C P AFY++ G +A +FV+ +LE GV Sbjct: 305 RDVVVAALNKV-GIACRVPTAAFYIWAKVPAGYGSSA----------EFVTAVLEKTGVV 353 Query: 362 VVHGSAFGLGPN--FRISYATSEALLEEACRRI 392 + G+ FG FRIS LEEA RI Sbjct: 354 LTPGNGFGTPGEGYFRISLTVDTDRLEEAVSRI 386 Lambda K H 0.318 0.134 0.402 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: 432 Number of extensions: 23 Number of successful extensions: 5 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: 400 Length of database: 389 Length adjustment: 31 Effective length of query: 369 Effective length of database: 358 Effective search space: 132102 Effective search space used: 132102 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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