Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate Pf1N1B4_4996 Aspartate aminotransferase (EC 2.6.1.1)
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4996 Length = 395 Score = 245 bits (626), Expect = 1e-69 Identities = 143/372 (38%), Positives = 212/372 (56%), Gaps = 9/372 (2%) Query: 14 SATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPEL 73 +A ++ +ALELR QGVD++ L+ G+PDFDTP + AA +L G T Y+ G L Sbjct: 15 AAAWKIHDRALELREQGVDVLLLSIGDPDFDTPLPIIHAAIDSLLAGDTHYSDVRGTRTL 74 Query: 74 REALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVR 133 R ++A + +R +G V + IV G + A++++ Q +LDPGDEVIV P +V+Y + Sbjct: 75 RSSIASRHQRRSGQLVDADHVIVLPGAQCAVYSVAQCLLDPGDEVIVAEPMYVTYEGVFG 134 Query: 134 FAGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLA 193 G VV V PE GF +P V IT +T+ +++NSPNNP+GA + +ALA L Sbjct: 135 ACGASVVPVAVRPENGFRVEPADVAALITSKTRVILLNSPNNPSGASLSLKSWKALAALC 194 Query: 194 VEHDFYLVSDEIYEHLLYEGEHFSPGRV--APEHTLTVNGAAKAFAMTGWRIGYACGPKE 251 V+HD +L+SDE+Y LL+EGEH SP + E T T+N +K+ AMTGWR+G+ GPK Sbjct: 195 VQHDLWLISDEVYSDLLFEGEHISPASLPGMAERTATINSLSKSHAMTGWRVGWMIGPKP 254 Query: 252 VIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTAL- 310 + + + +S Q A AL + V + RE YR+RRDL+ L+ Sbjct: 255 LAEHLMHLSLCMLFGLPDFVQNAAQVAL---DKDLPEVALMREEYRQRRDLVCARLSGCP 311 Query: 311 GLKAVRPSGAFYVLMDTSPIAPDEVRAAERLLEA-GVAVVPGTDF--AAFGHVRLSYATS 367 G++ ++P G +V++D AERLLE GV+V+ G F +A GH+R+ Sbjct: 312 GIRPIKPDGGMFVMVDVRQTGLGAQDFAERLLEGYGVSVLAGEAFGPSAAGHIRIGLVVD 371 Query: 368 EENLRKALERFA 379 + L A +R A Sbjct: 372 QARLADACQRIA 383 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: 362 Number of extensions: 14 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: 395 Length adjustment: 31 Effective length of query: 354 Effective length of database: 364 Effective search space: 128856 Effective search space used: 128856 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