Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate 16484 b2379 hypothetical protein (NCBI)
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Keio:16484 Length = 412 Score = 154 bits (390), Expect = 3e-42 Identities = 115/381 (30%), Positives = 179/381 (46%), Gaps = 17/381 (4%) Query: 7 RVQAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTK-YA 65 R+ + P + RR+G D++ + G PD TP H+ E + T Y+ Sbjct: 12 RIDRLPPYVFNITAELKMAARRRGEDIIDFSMGNPDGATPPHIVEKLCTVAQRPDTHGYS 71 Query: 66 PPAGIPELREALAEKFRRENGLSVTPE-ETIVTVGGKQALFNLFQAILDPGDEVIVLSPY 124 GIP LR A++ ++ + + PE E IVT+G K+ L +L A LD GD V+V +P Sbjct: 72 TSRGIPRLRRAISRWYQDRYDVEIDPESEAIVTIGSKEGLAHLMLATLDHGDTVLVPNPS 131 Query: 125 WVSYPEMVRFAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKE 184 + + AG V V + F + ER R P+ K +++ P+NPT E Sbjct: 132 YPIHIYGAVIAGAQVRSVPLVEGVDFFNELERAIRESYPKPKMMILGFPSNPTAQCVELE 191 Query: 185 VLEALARLAVEHDFYLVSDEIYEHLLYEGEHFS-----PGRVAPEHTLTVNGAAKAFAMT 239 E + LA +D +V D Y ++Y+G PG A + + +K++ M Sbjct: 192 FFEKVVALAKRYDVLVVHDLAYADIVYDGWKAPSIMQVPG--ARDVAVEFFTLSKSYNMA 249 Query: 240 GWRIGYACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRR 299 GWRIG+ G K ++ A+A + S T Q A + AL E + V E Y+RR Sbjct: 250 GWRIGFMVGNKTLVSALARIKSYHDYGTFTPLQVAAIAAL---EGDQQCVRDIAEQYKRR 306 Query: 300 RDLLLEGLTALGLKAVRPSGAFYV--LMDTSPIAPDEVRAAERLL-EAGVAVVPGTDFAA 356 RD+L++GL G P + YV + A + A++LL EA V V PG F Sbjct: 307 RDVLVKGLHEAGWMVEMPKASMYVWAKIPEPYAAMGSLEFAKKLLNEAKVCVSPGIGFGD 366 Query: 357 FG--HVRLSYATSEENLRKAL 375 +G HVR + + + +R+A+ Sbjct: 367 YGDTHVRFALIENRDRIRQAI 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: 358 Number of extensions: 18 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: 412 Length adjustment: 31 Effective length of query: 354 Effective length of database: 381 Effective search space: 134874 Effective search space used: 134874 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