Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78 (characterized)
to candidate AO356_16100 AO356_16100 aminotransferase
Query= SwissProt::Q8KDS8 (400 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_16100 Length = 390 Score = 193 bits (491), Expect = 6e-54 Identities = 130/391 (33%), Positives = 195/391 (49%), Gaps = 17/391 (4%) Query: 11 SRRVLSMQESQTMKITGLAKKMQAEGKDVVSLSAGEPDFPTPENVCEAGIEAIRKGFTRY 70 S R +++ M + A ++QA G DV+ L GEPDF T E + +AG A+ G TRY Sbjct: 6 SARSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPIIQAGQAALAAGKTRY 65 Query: 71 TANSGIPELKKAIIRKLQRDNGLEYAEDEIIVSNGGKQALANTFLALCDEGDEVIVPAPY 130 TA GIPEL++AI + G++ I+++ GG AL T L D G ++ P Sbjct: 66 TAARGIPELREAISGFYGQRYGVDIDPRRIMITPGGSGALLLTSALLVDPGKHWLLADPG 125 Query: 131 WVSFPEMARLAEATPVIVETSIETGYKMTPEQLAAAITPKTRILVLNSPSNPSGAVYNEA 190 + RL E +V + Y++TP+ + + ++ SP+NP+G + Sbjct: 126 YPCNRHFLRLVEGAAQLVPVGADVRYQLTPDLVDRHWDQDSVGALVASPANPTGTILTRD 185 Query: 191 EVRALMQVIEGKEIFVLSDEMYDMICYGGVRPFSPARIPEMKPWVIVSNGTSKSYSMTGW 250 E+ L + I+G ++ DE+Y + YG A + E+ V N SK + MTGW Sbjct: 186 ELAGLSKAIKGHNGHLVVDEIYHGLTYG----TDAASVLEVDDDAFVLNSFSKYFGMTGW 241 Query: 251 RIGYLAAPKWIINACDKIQSQTTSNANSIAQKAAVAALD-GDQSIVEQRRAEFEKRRDFM 309 R+G+L AP I +K+ +A S+AQ AA+A + I EQRRAEF RRDF+ Sbjct: 242 RLGWLVAPSAAIGELEKLAQNLYISAPSMAQYAALACFEPATIEIFEQRRAEFALRRDFL 301 Query: 310 FRELNTISGIECTLPEGAFYIFPSIKGLLGKTFGGKVMKDSTDVAEYLLTEHYVATVPGD 369 L + P+GAFY++ I TFGG D+ ++ L +VA PG Sbjct: 302 LPALRELGFGIAVEPQGAFYLYADI-----STFGG----DAFAFCQHFLETEHVAFTPGL 352 Query: 370 AFG---APENLRLSYAASIEELAEAVNRIRK 397 FG A ++R +Y S+ L EAV RI + Sbjct: 353 DFGRHQASHHVRFAYTQSLPRLQEAVARIER 383 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: 346 Number of extensions: 13 Number of successful extensions: 4 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: 390 Length adjustment: 31 Effective length of query: 369 Effective length of database: 359 Effective search space: 132471 Effective search space used: 132471 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