Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__SynE:Synpcc7942_0645 Length = 453 Score = 146 bits (369), Expect = 1e-39 Identities = 112/345 (32%), Positives = 156/345 (45%), Gaps = 30/345 (8%) Query: 4 RTLEDWRALLEAEKTLDSGVYNK---------HDLLIVRGQGARVWDAEGNEYIDCVGGY 54 +T++ A+K + GV + ++ R + A WD +GN YID VG + Sbjct: 28 KTIKSDEIFAAAQKLMPGGVSSPVRAFKSVGGQPIVFDRVKDAYAWDVDGNRYIDYVGTW 87 Query: 55 GVANLGHGNPEVVEAVKRQAE--TLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNS 112 G A GH +PEV+EA+K E T P L + + P + V VNS Sbjct: 88 GPAICGHAHPEVIEALKVAMEKGTSFGAPCALENVL-----AEMVIDAVPSIEMVRFVNS 142 Query: 113 GTEANEAALKFARAHTGRKKFVAAMRGFSGR-----TMGSLSVTWEPKYREPFLPLVEPV 167 GTEA A L+ RA+TGR K + + G V P +P Sbjct: 143 GTEACMAVLRLMRAYTGRDKIIKFEGCYHGHADMFLVKAGSGVATLGLPDSPGVPKSTTA 202 Query: 168 EFI--PYNDVEALKRAVDE---ETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALL 222 + PYND+EA+K E E A VILEP+ G G FL REIT E ALL Sbjct: 203 NTLTAPYNDLEAVKALFAENPGEIAGVILEPIVGNSGFIVPDAGFLEGLREITLEHDALL 262 Query: 223 ILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGG--- 279 + DE+ TG R E FG+ PD+ TL K +GGG+P+G + E+ + + G Sbjct: 263 VFDEVMTGF-RIAYGGVQEKFGVTPDLTTLGKIIGGGLPVGAYGGKREIMQLVAPAGPMY 321 Query: 280 HGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAI 324 T GNPLAM AG+ + L + +E ++ + L AI Sbjct: 322 QAGTLSGNPLAMTAGIKTLELLRQPGTYEYLDQITKRLSDGLLAI 366 Lambda K H 0.319 0.137 0.403 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: 400 Number of extensions: 27 Number of successful extensions: 6 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: 395 Length of database: 453 Length adjustment: 32 Effective length of query: 363 Effective length of database: 421 Effective search space: 152823 Effective search space used: 152823 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 (21.7 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