Align ornithine δ-aminotransferase (EC 2.6.1.13) (characterized)
to candidate Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase
Query= metacyc::MONOMER-16810 (468 letters) >FitnessBrowser__SynE:Synpcc7942_0645 Length = 453 Score = 135 bits (340), Expect = 3e-36 Identities = 90/299 (30%), Positives = 145/299 (48%), Gaps = 27/299 (9%) Query: 54 PMVFSKAKDVHVWDPEGRKYLDFLSAYSAVNQGHCHEKILNALSQQAQQLTLSSR--AFH 111 P+VF + KD + WD +G +Y+D++ + GH H +++ AL ++ T A Sbjct: 61 PIVFDRVKDAYAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEKGTSFGAPCALE 120 Query: 112 NDIFPIFAQHLTSMFGYEMILPMNTGAEGVETALKLARKWGYEKKHIPKNEAIIISCCGC 171 N + + + S+ EM+ +N+G E L+L R + K II GC Sbjct: 121 NVLAEMVIDAVPSI---EMVRFVNSGTEACMAVLRLMRAYTGRDK--------IIKFEGC 169 Query: 172 FHGRTTAVISMSCDNEATRGFGPFLPGL--------LKVDFGDADSLKSMFEAHGDKVAG 223 +HG + + AT G P PG+ L + D +++K++F + ++AG Sbjct: 170 YHGHADMFLVKAGSGVATLGL-PDSPGVPKSTTANTLTAPYNDLEAVKALFAENPGEIAG 228 Query: 224 FLFEPIQGEAGVIVPPKGYLQSVRELCSKYNVLMIADEIQTGIGRTGKLLACEWESVRPD 283 + EPI G +G IVP G+L+ +RE+ +++ L++ DE+ TG R E V PD Sbjct: 229 VILEPIVGNSGFIVPDAGFLEGLREITLEHDALLVFDEVMTGF-RIAYGGVQEKFGVTPD 287 Query: 284 VVILGKALGGGVLPVSAVLADKDIMLCFKPG---EHGSTFGGNPLASAVAIAALEIVEE 339 + LGK +GGG LPV A ++IM P T GNPLA I LE++ + Sbjct: 288 LTTLGKIIGGG-LPVGAYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQ 345 Lambda K H 0.319 0.136 0.405 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: 456 Number of extensions: 27 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: 468 Length of database: 453 Length adjustment: 33 Effective length of query: 435 Effective length of database: 420 Effective search space: 182700 Effective search space used: 182700 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: 51 (24.3 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