Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate Pf6N2E2_5161 Valine--pyruvate aminotransferase (EC 2.6.1.66) ## AvtA
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5161 Length = 390 Score = 199 bits (507), Expect = 8e-56 Identities = 132/383 (34%), Positives = 190/383 (49%), Gaps = 8/383 (2%) Query: 5 SRRVQAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKY 64 S R +A++P +A+ A+A EL+ G D++ L GEPDF T E + +A + ALA GKT+Y Sbjct: 6 SARSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPIIQAGQAALAAGKTRY 65 Query: 65 APPAGIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPY 124 GIPELREA+A + + G+ + P +VT GG AL ++DPG ++ P Sbjct: 66 TAARGIPELREAIAGFYGQRYGVEIDPRRILVTPGGSGALLLASALLVDPGKHWLLADPG 125 Query: 125 WVSYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKE 184 + +R G V PE + P+ V R + +V SP NPTG + ++ Sbjct: 126 YPCNRHFLRLVEGAAQLVPVGPEVRYQLTPDLVNRHWDQDSVGALVASPANPTGTILTRD 185 Query: 185 VLEALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIG 244 L L+++ H+ +LV DEIY L Y + S V + +N +K F MTGWR+G Sbjct: 186 ELAGLSKVIKGHNGHLVVDEIYHGLTYGTDAASVLEV-DDDAFVLNSFSKYFGMTGWRLG 244 Query: 245 YACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLL 304 + P + + ++ S ++AQ+A L + A+ E R + RRRD LL Sbjct: 245 WLVAPSAAVGELEKLAQNLYISAPSMAQYAALACF--EPATIEIFEQRRAEFARRRDFLL 302 Query: 305 EGLTALGLK-AVRPSGAFYVLMDTSPIAPDEVRAAERLLEA-GVAVVPGTDFA---AFGH 359 L LG AV P GAFY+ D S D + LE VA PG DF A H Sbjct: 303 PALRELGFGIAVEPEGAFYLYADISAFGGDAFAFCQHFLETEHVAFTPGLDFGRHQAGHH 362 Query: 360 VRLSYATSEENLRKALERFARVL 382 VR +Y S L +A+ R R L Sbjct: 363 VRFAYTQSLPRLEEAVARIERGL 385 Lambda K H 0.317 0.133 0.379 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: 379 Number of extensions: 19 Number of successful extensions: 3 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: 385 Length of database: 390 Length adjustment: 30 Effective length of query: 355 Effective length of database: 360 Effective search space: 127800 Effective search space used: 127800 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