Align glutamine-pyruvate transaminase (EC 2.6.1.15); kynurenine-oxoglutarate transaminase (EC 2.6.1.7); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= BRENDA::Q71RI9 (455 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 165 bits (417), Expect = 3e-45 Identities = 120/405 (29%), Positives = 188/405 (46%), Gaps = 60/405 (14%) Query: 23 SSSKVLGLCTSAKMALKFKNAKRIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYV 82 S S L + AK A + EGLD V + G PD P ++ Sbjct: 11 SPSLTLAIAAQAK-------AMKAEGLD---------------VCSFSAGEPDFETPLHI 48 Query: 83 KEELSKAAFIDNMNQYTRGFGHP----ALVKALSCLYGKIYQRQIDPNEEILVAVGAYGS 138 + ++A + +Y G P A+ + L G YQ ILV G S Sbjct: 49 RNAAAQA-LAEGKTRYGPAAGEPDLREAIAQKLRADNGLDYQAA-----NILVTNGGKQS 102 Query: 139 LFNSIQGLVDPGDEVIIMVPFYDCYEPMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDP 198 L+N +Q L+DPGDEVII P++ Y MV++AG VPV + + +DG K P Sbjct: 103 LYNLMQVLLDPGDEVIIPAPYWLSYPEMVKLAGGVPVIV--ETFASDGFK-------LQP 153 Query: 199 RELESKFSSKTKAIILNTPHNPLGKVYTRQELQVIADLCVKHDTLCISDEVYEWLVYTGH 258 ++L + +T+ ++LN+P NP G VY+RQEL+ IA + HD +SDE+YE ++Y G Sbjct: 154 QQLAGAITPRTRLLVLNSPSNPTGMVYSRQELEAIAPIIEAHDFWVVSDEIYEKILYDGA 213 Query: 259 THVKIATL-PGMWERTITIGSAGKTFSVTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATP 317 H I +L P +ERT+ K +S+TGW++G+ GP+ LI ++Q +S T Sbjct: 214 DHHSIGSLSPACFERTLISNGFAKAYSMTGWRVGYLAGPSELIAAAASLQSHSTSNVCTF 273 Query: 318 LQAALAEAFWIDIKRMDDPECYFNSLPKELEVKRDRMVRLLNSV-GLKPIVPDGGYFIIA 376 Q I + P+ + +R ++ LN + GL +P+G +++ Sbjct: 274 AQYGA-------IAALQGPQDCVAEMLAAFTERRQLILNGLNQIAGLSCPIPEGAFYVFV 326 Query: 377 DVSSLGADLSDMNSDEPYDYKFVKWMTKHKKLTAIPVSAFCDSKS 421 D+S G D + + + ++ AIP AF D +S Sbjct: 327 DISKTGLD----------SMTYCRQLLDQHQVAAIPGIAFGDDRS 361 Lambda K H 0.320 0.136 0.419 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: 394 Number of extensions: 20 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: 455 Length of database: 392 Length adjustment: 32 Effective length of query: 423 Effective length of database: 360 Effective search space: 152280 Effective search space used: 152280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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