Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate CA265_RS11675 CA265_RS11675 aspartate aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__Pedo557:CA265_RS11675 Length = 399 Score = 157 bits (396), Expect = 7e-43 Identities = 95/298 (31%), Positives = 153/298 (51%), Gaps = 5/298 (1%) Query: 30 GRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTKYTAVDGIPELKRAICEKFERENGLKY 89 G+ V L G+PD +TP+ + A K ID YT +G + + E + + G Sbjct: 30 GKKVFHLNIGQPDIETPEGMLNAIKN-IDFNVWAYTPSEGTLAYRLKLTEYYNKL-GYNI 87 Query: 90 TPAQVTVGTGGKQILYNALVATLNPGDEVIIPAPYWVSYPDMVLLAGGTPVSVAAGMETG 149 TP + V GG + + A+ +N GDE+IIP P++ +Y ++ + + +E G Sbjct: 88 TPENILVTVGGSEAITIAMQTCVNEGDEIIIPEPFYANYNGFACMSNVVVKPILSYIENG 147 Query: 150 FKLTP-EQLEAAITPRTKWFIFNSPSNPTGAAYTRAELAALCEVLMRHPQVWIMSDDMYE 208 F L P + E IT +TK I +P+NPTG Y+RAEL AL + +++ +++ SD+ Y Sbjct: 148 FALPPIAEFEKLITEKTKAIIICNPNNPTGYLYSRAELEALKTLCVKY-DLFLFSDEAYR 206 Query: 209 HLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCMTGWRIGYAAGPVELIRAMGTIQSQS 268 +D +F +P ++ GL + + + VSK Y G R+G + + A G +Q+ Sbjct: 207 EFCYDGREFISPMHLD-GLDENVVIMDTVSKRYSACGARLGCLITKNKEVIASGLKFAQA 265 Query: 269 TSNPCSIAQYAALEALSGPQEFLATNREAFQRRRDLVVSMLNEAKGVTCPNPEGAFYV 326 +P + Q A A+ P + + RRD +V LN+ +GV CPNP GAFYV Sbjct: 266 RLSPGMVEQIAGAAAVDTPDSYFEKVNTEYTLRRDTLVGRLNQIEGVFCPNPGGAFYV 323 Lambda K H 0.318 0.134 0.399 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: 463 Number of extensions: 30 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: 399 Length adjustment: 31 Effective length of query: 369 Effective length of database: 368 Effective search space: 135792 Effective search space used: 135792 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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