Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_011021821.1 MA_RS09470 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000007345.1:WP_011021821.1 Length = 380 Score = 323 bits (829), Expect = 4e-93 Identities = 169/383 (44%), Positives = 246/383 (64%), Gaps = 13/383 (3%) Query: 5 SRRVQAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKY 64 S R++ ++ SAT+ ++ A + ++G D++ + GEPDFDTP+++ +AA +A+ +GKT Y Sbjct: 3 SARLKRVEESATIRISNIATRMIKEGTDVINFSLGEPDFDTPKNICDAAAKAMYEGKTHY 62 Query: 65 APPAGIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPY 124 AP AGIPELR A+AEK + EN L VT ++ +VT G KQA+F + LD GD ++ P Sbjct: 63 APSAGIPELRAAIAEKLKTENHLEVTEKDVLVTPGAKQAIFEIMMGALDDGDRALLFDPA 122 Query: 125 WVSYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKE 184 WV+Y +RF+G V V T+PE GF+PD I +TK +VVNSP NPTG V+ K+ Sbjct: 123 WVTYDACIRFSGANTVWVPTVPERGFLPD--NFAEYINDKTKLIVVNSPGNPTGGVFGKK 180 Query: 185 VLEALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGRV--APEHTLTVNGAAKAFAMTGWR 242 L+ +A LA++HD +VSDEIYE ++Y+ EH S G + T+TVNG +KA+AMTGWR Sbjct: 181 TLQCIADLAIDHDLLVVSDEIYEKIIYDREHISIGSFDGMQDRTITVNGFSKAYAMTGWR 240 Query: 243 IGYACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTN-QEASRAFVEMAREAYRRRRD 301 +GY P E+ K + + S S +S T Q+ LEAL Q+ +A V + ++ RRD Sbjct: 241 LGYLTAPPEIFKLLQKIQSHSVSSATTFVQYGGLEALQGPQDGVKAMV----DRFKMRRD 296 Query: 302 LLLEGLTALGLKAVRPSGAFYVLMDTSPIAPDEVRAAERLL-EAGVAVVPGTDFAAFGH- 359 +L++GL +G++ +P GAFY + S + AERLL EA VAV PG F A G Sbjct: 297 ILIDGLNKIGIECKKPDGAFYAFANVSEYG-NGTEVAERLLKEAHVAVTPGIAFGASGED 355 Query: 360 -VRLSYATSEENLRKALERFARV 381 +R+SYATS + +R+ALER ++ Sbjct: 356 FIRISYATSIDRIREALERLEKI 378 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: 403 Number of extensions: 19 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: 380 Length adjustment: 30 Effective length of query: 355 Effective length of database: 350 Effective search space: 124250 Effective search space used: 124250 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