Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_011734975.1 PPRO_RS05105 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000015045.1:WP_011734975.1 Length = 398 Score = 178 bits (451), Expect = 3e-49 Identities = 132/369 (35%), Positives = 195/369 (52%), Gaps = 23/369 (6%) Query: 26 LRRQGVD--LVALTAGEPDFDTPEHVKE---AARRALAQGKTKYAPPAGIPELREALAEK 80 LRR+ D + T G PD + P+ +E A R G +Y AG PE R A+A K Sbjct: 27 LRREFGDESVYDFTLGNPDVEPPQAFQEELLALARNPLPGMHRYMNNAGYPETRAAVAAK 86 Query: 81 FRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVV 140 R++G+ +T E I+T G AL + + IL+PG+EVI+L+PY+V Y + GGV V Sbjct: 87 LARDSGIDLTAEHVIMTCGAGGALNVVLKTILNPGEEVIILAPYFVEYKFYIDNHGGVPV 146 Query: 141 EVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVE----- 195 V T + F D E + +AIT +T+A+++ SPNNPTG +YP E L L + + Sbjct: 147 PVWT-DHQTFQLDIEAIEQAITLKTRAILICSPNNPTGVIYPAESLARLGEVVKKVHKRN 205 Query: 196 -HDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIGY-ACGPK--E 251 H Y++SDE Y + Y+G+ E ++ V +K A+ G RIGY A P+ Sbjct: 206 GHLIYVISDEPYARIAYDGKQVPNIFPLIESSVIVTSHSKDLALPGERIGYLAANPRMDT 265 Query: 252 VIKAMASVSSQSTTSPDTIAQWATLEALTN-QEASRAFVEMAREAYRRRRDLLLEGLTAL 310 V++ MA + A +TN Q+ S V++A AY+ +RDLL+ LTAL Sbjct: 266 VMQFMAGAVFSNRVLGFVNAPALMQRLVTNLQDES---VDIA--AYQDKRDLLVRELTAL 320 Query: 311 GLKAVRPSGAFYVLMDTSPIAPDEVRAAERLLEAGVAVVPGTDFAAFGHVRLSYATSEEN 370 G K V P GAFY L SP+A D+V + + + +VPG F A G R++Y Sbjct: 321 GFKMVIPDGAFY-LFPQSPLA-DDVAFVKLAQKHHILLVPGAGFGAPGFFRIAYCVDRAV 378 Query: 371 LRKALERFA 379 + ++L +A Sbjct: 379 IERSLPAWA 387 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: 376 Number of extensions: 20 Number of successful extensions: 5 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: 398 Length adjustment: 31 Effective length of query: 354 Effective length of database: 367 Effective search space: 129918 Effective search space used: 129918 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 10 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