Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_086510442.1 BZY95_RS13490 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_002151265.1:WP_086510442.1 Length = 386 Score = 212 bits (539), Expect = 2e-59 Identities = 136/383 (35%), Positives = 195/383 (50%), Gaps = 8/383 (2%) Query: 7 RVQAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAP 66 RV + P +++ A G D++ L GEPDF TPE V A + ALA G T+Y+P Sbjct: 6 RVDRVAPFRVMSLLEAAQAREAAGHDVIHLEVGEPDFATPEPVVAAGQAALAAGLTRYSP 65 Query: 67 PAGIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWV 126 AG+P LREA+A + G V P +VT G AL Q ++ PGD V++ P + Sbjct: 66 AAGLPALREAIAGHYGEHFGADVDPRRVLVTPGASGALLLASQLLVGPGDRVLMADPNYP 125 Query: 127 SYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVL 186 + AG V V P+ G+ D V R T+ ++ +P+NPTG + L Sbjct: 126 CNRHFMALAGAEVDTVPIGPQSGWQLDANLVARHWQDATRLAMLATPSNPTGHMLDAAQL 185 Query: 187 EALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRVAPEHTLTVNGAAKAFAMTGWRIGYA 246 +A+A +L+ DEIY+ L Y+ S + + VN +K F MTGWR+G+ Sbjct: 186 KAVADTVAARGGHLLVDEIYQGLSYDIAPLSVASLTAD-AFVVNSFSKYFGMTGWRLGWL 244 Query: 247 CGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEG 306 P+ ++ + ++ + T AQ A L A T + RA +E R RRRD LL G Sbjct: 245 LAPQAAVEPLTRLAQNVFLAAPTPAQHAALAAFTPE--CRALLEARRSELGRRRDALLAG 302 Query: 307 LTALGL-KAVRPSGAFYVLMDTSPIAPDEVRAAERLL-EAGVAVVPGTDFAAFG---HVR 361 L LGL ++ P GAFY+ +D S + D +RLL E VA+ PG DFA G HVR Sbjct: 303 LARLGLAPSLPPQGAFYLWLDISRYSRDSQAFCQRLLEEENVAITPGIDFAVTGGEYHVR 362 Query: 362 LSYATSEENLRKALERFARVLGR 384 +++ T E L +A+ R R L R Sbjct: 363 IAFTTGIERLEEAVSRLERFLAR 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: 375 Number of extensions: 15 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: 385 Length of database: 386 Length adjustment: 30 Effective length of query: 355 Effective length of database: 356 Effective search space: 126380 Effective search space used: 126380 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