Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_037575899.1 BS73_RS24325 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000744815.1:WP_037575899.1 Length = 398 Score = 225 bits (574), Expect = 1e-63 Identities = 142/362 (39%), Positives = 197/362 (54%), Gaps = 17/362 (4%) Query: 34 VALTAGEPDFDTPEHVKEAARRALAQGK-TKYAPPAGIPELREALAEKFRRENGLSVTPE 92 + L G PD D PE V+EAA RAL +G+ +Y P G+PELR A+AE R GL P+ Sbjct: 42 INLGQGFPDTDGPEAVREAAVRALREGRGNQYPPGPGVPELRAAVAEHQLRFYGLDFDPD 101 Query: 93 -ETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFV 151 E +VT G +A+ A+L+PGDEVI P++ SY + AG V TL F Sbjct: 102 TEVLVTAGATEAIAASMLALLEPGDEVIAFEPFYDSYAACIAMAGAKRVPF-TLRAPSFR 160 Query: 152 PDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLY 211 PD + +R ITP T+ L++NSP+NPTG V E L A+A LAVEHD +V+DE+YEHL++ Sbjct: 161 PDLDELRALITPSTRLLLLNSPHNPTGMVLDDEELRAIAALAVEHDLLVVTDEVYEHLVF 220 Query: 212 EGEHFSPGRVAP---EHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPD 268 EG H P P E T++++ A K F+ TGW++G+ ++ A+ + T Sbjct: 221 EGAH-RPIAALPGMRERTVSISSAGKTFSFTGWKVGWVTAAAPLVAAVRTAKQYLTYVSA 279 Query: 269 TIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTS 328 Q+A EAL + A+ E R + RRRRDLL GL A G + P G +++ D + Sbjct: 280 GPFQYAVAEALRLPD---AYYEDFRASLRRRRDLLDAGLRAAGFEVYEPQGTYFITTDIA 336 Query: 329 PIAPDEVRAAERLL--EAGVAVVPGTDF-----AAFGHVRLSYATSEENLRKALERFARV 381 P + A R L GV VP + F A VR ++ EE LR+A R R+ Sbjct: 337 PFGAKDAYAFCRSLPERCGVVAVPNSVFYDDPEAGRSQVRFTFCKKEEVLREAAARLQRL 396 Query: 382 LG 383 G Sbjct: 397 RG 398 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: 449 Number of extensions: 31 Number of successful extensions: 6 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 Jul 26 2024. The underlying query database was built on Jul 25 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