Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate GFF4665 PS417_23870 aminotransferase
Query= curated2:O33822 (383 letters) >FitnessBrowser__WCS417:GFF4665 Length = 390 Score = 195 bits (495), Expect = 2e-54 Identities = 125/384 (32%), Positives = 192/384 (50%), Gaps = 8/384 (2%) Query: 5 SQRVKSMKPSATVAVNARALELRRKGVDLVALTAGEPDFDTPEHVKEAGRRALAQGKTKY 64 S R ++++P +A+ ARA EL+ G D++ L GEPDF T E + +AG+ ALA GKT+Y Sbjct: 6 SARSRAIEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPIIKAGQAALANGKTRY 65 Query: 65 APPAGIPELREAVAEKFRRENGLEVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLAPY 124 G+PELREA++ +++ GL V P ++T GG AL ++DPG ++ P Sbjct: 66 TAARGLPELREAISGFYQQRYGLNVDPARILITPGGSGALLLASSLLVDPGKHWLLADPG 125 Query: 125 WVSYPEMVRFAGGVPVEVPTLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGVVYPEE 184 + +R G VP PE + + V + + +V SP NPTG + + Sbjct: 126 YPCNRHFLRLVEGAAQLVPVGPEVRYQLTADLVAKHWNQDSVGALVASPANPTGTILTRD 185 Query: 185 VLRALAEMALQHDFYLVSDEIYEHLIYEGAHFSPGTLAPEHTITVNGAAKAFAMTGWRIG 244 L L+ + +LV DEIY L Y G + + +N +K F MTGWR+G Sbjct: 186 ELAGLSAAIKARNGHLVVDEIYHGLTY-GTDAASVLEVDDEAFVLNSFSKYFGMTGWRLG 244 Query: 245 YACGPKAVIKAMADVSSQSTTSPDTIAQWATLEALTNREASMAFIAMAREAYRKRRDLLL 304 + P A + + ++ S ++AQ A L T + +++ + R + +RRD LL Sbjct: 245 WLVAPPAAVGELEKLAQNLYISAPSMAQHAALACFTPQ--TLSILEERRAEFGRRRDFLL 302 Query: 305 EGLSRIGLE-AVRPSGAFYVLMDTSPFAPNEVEAAERLL-MAGVAVVPGTEFAAF---GH 359 L +G AV P GAFY+ D S F + L VA PG +F F H Sbjct: 303 PALRELGFGIAVEPEGAFYLYADISAFGGDAFAFCRHFLETEHVAFTPGLDFGRFKAGHH 362 Query: 360 VRLSYATGEENLKKALERFAQALQ 383 VR +Y + L++A+ER A+ L+ Sbjct: 363 VRFAYTQNLDRLQEAVERIARGLR 386 Lambda K H 0.317 0.133 0.382 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: 369 Number of extensions: 18 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: 383 Length of database: 390 Length adjustment: 30 Effective length of query: 353 Effective length of database: 360 Effective search space: 127080 Effective search space used: 127080 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