Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= BRENDA::Q8YMS6 (388 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 540 bits (1390), Expect = e-158 Identities = 269/386 (69%), Positives = 320/386 (82%) Query: 1 MKLAARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGK 60 MKL+ RV +V+PS+TLAIAA+AKAMKAEG+DVCSFSAGEPDF+TP HI+ AAA+AL EGK Sbjct: 1 MKLSERVGRVSPSLTLAIAAQAKAMKAEGLDVCSFSAGEPDFETPLHIRNAAAQALAEGK 60 Query: 61 TKYGAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIP 120 T+YG AAGEP LREAIA+KL+ DN LDY+ N++VTNGGK SLYNL+ L+DPGDEVIIP Sbjct: 61 TRYGPAAGEPDLREAIAQKLRADNGLDYQAANILVTNGGKQSLYNLMQVLLDPGDEVIIP 120 Query: 121 APYWLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVY 180 APYWLSYPEMV L GG VIV T AS G+K+ P+QL AITP+T+L VLNSPSNPTGMVY Sbjct: 121 APYWLSYPEMVKLAGGVPVIVETFASDGFKLQPQQLAGAITPRTRLLVLNSPSNPTGMVY 180 Query: 181 TPEEIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYS 240 + +E++A+A ++ D +VVSDEIYEKILYDGA H SIGSL F RTLISNGFAKAYS Sbjct: 181 SRQELEAIAPIIEAHDFWVVSDEIYEKILYDGADHHSIGSLSPACFERTLISNGFAKAYS 240 Query: 241 MTGWRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDCVEEMRQAFAKRR 300 MTGWR+GYLAGP ++I AA+S+Q HSTSNVCTFAQYGAIAAL+ QDCV EM AF +RR Sbjct: 241 MTGWRVGYLAGPSELIAAAASLQSHSTSNVCTFAQYGAIAALQGPQDCVAEMLAAFTERR 300 Query: 301 QVMLDRLNAIPGLSTAKPDGAFYLFPDISKTGLKSLEFCDALIEEHKVAVIPGIAFGADD 360 Q++L+ LN I GLS P+GAFY+F DISKTGL S+ +C L+++H+VA IPGIAFG D Sbjct: 301 QLILNGLNQIAGLSCPIPEGAFYVFVDISKTGLDSMTYCRQLLDQHQVAAIPGIAFGDDR 360 Query: 361 NIRLSYATDLATIEKGLDRLEKFVRS 386 +IRLSYATD TIEKGL+RL+ F S Sbjct: 361 SIRLSYATDCQTIEKGLERLQLFQNS 386 Lambda K H 0.317 0.134 0.381 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: 439 Number of extensions: 10 Number of successful extensions: 1 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: 388 Length of database: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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 (21.6 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