Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78 (characterized)
to candidate 8502179 DvMF_2889 aspartate aminotransferase (RefSeq)
Query= SwissProt::Q8KDS8 (400 letters) >FitnessBrowser__Miya:8502179 Length = 394 Score = 138 bits (347), Expect = 3e-37 Identities = 111/389 (28%), Positives = 179/389 (46%), Gaps = 39/389 (10%) Query: 27 GLAKKMQAEGKDVVSLSAGEPDFPTPENVCEAGIEAIRKG---FT-RYTANSGIPELKKA 82 G+A K Q + V S G PD P P V +A E FT Y N G P + Sbjct: 25 GIALKQQYGEEAVCDFSLGNPDLPAPPAVGQALRELADHAGEPFTFGYMPNGGYPWARAK 84 Query: 83 IIRKLQRDNGLEYAEDEIIVSNGGKQALANTFLALCDEGDEVIVPAPYWVSFPEMARLAE 142 + L + G++ A D+++++ G L A+ + GDEV+ +P++V + Sbjct: 85 LAAHLSAEQGVDLAADDVVLTCGAAGGLNAFLRAVLEPGDEVLAVSPFFVEYGFYVANHG 144 Query: 143 ATPVIVETSIETGYKMTPEQLAAAITPKTRILVLNSPSNPSGAVYNEAEVRALMQVI--- 199 T V + +T + + + AAI P+TR L++NSP+NP+G +YN AE+ L + Sbjct: 145 GTFRTVPSKPDT-FALDVAAIEAAIGPRTRALIINSPNNPTGVIYNRAELTELAAALGRA 203 Query: 200 ---EGKEIFVLSDEMYDMICYGGVRPFSPARIPEMKPWVIVSNGTSKSYSMTGWRIGYLA 256 G+ IF++SDE Y + Y G P+ +P + V++S+ SK+ S+ G R+GY+A Sbjct: 204 SQKHGRPIFLISDEPYRFLSYDGDE--VPSLLPLYQHAVVISS-FSKNLSLAGERLGYIA 260 Query: 257 AP-----KWIINACDKIQSQTTS--NANSIAQKAAVAALDGDQSIVEQRRAEFEKRRDFM 309 + + A + ++ N ++ Q AL + + +RRD M Sbjct: 261 LSPLMEGRSTLTAALLLTNRILGFVNPPAVGQHLMAKALGS-----QVDAGIYARRRDMM 315 Query: 310 FRELNTISGIECTLPEGAFYIFPSIKGLLGKTFGGKVMKDSTDVAEYLLTEHYVATVPGD 369 R L +G E +P GAFY FP G F ++M E V VPG Sbjct: 316 ARILRD-AGYEFQMPAGAFYFFPKAPGGDDVKFVNRLM------------EEKVLAVPGS 362 Query: 370 AFGAPENLRLSYAASIEELAEAVNRIRKA 398 FG P + RL++ + +A + R+A Sbjct: 363 GFGGPGHFRLTFCVGEDVIARSEEGFRRA 391 Lambda K H 0.316 0.132 0.376 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: 372 Number of extensions: 22 Number of successful extensions: 7 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: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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 (21.6 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