Align [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) (characterized)
to candidate Synpcc7942_0645 Synpcc7942_0645 glutamate-1-semialdehyde aminotransferase
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__SynE:Synpcc7942_0645 Length = 453 Score = 131 bits (329), Expect = 4e-35 Identities = 100/302 (33%), Positives = 143/302 (47%), Gaps = 26/302 (8%) Query: 21 YVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISILSTSFSTPIKDEMLQA-- 78 Y WD++G RY+D+ G A GH +P ++E LK +E TSF P E + A Sbjct: 71 YAWDVDGNRYIDYVGTWGPAICGHAHPEVIEALKVAMEK----GTSFGAPCALENVLAEM 126 Query: 79 -LDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKKIIAFKNAFHGRT------AGSL 131 +D V +M +NSGTEA A L+ R TGR KII F+ +HG AGS Sbjct: 127 VIDAVPSIEM--VRFVNSGTEACMAVLRLMRAYTGRDKIIKFEGCYHGHADMFLVKAGSG 184 Query: 132 SVTWNKKYREPFEPLVGPVEFLT--FNNIEDLSKI----DNETAAVIVEPIQGESGVIPA 185 T P P LT +N++E + + E A VI+EPI G SG I Sbjct: 185 VATLGLP-DSPGVPKSTTANTLTAPYNDLEAVKALFAENPGEIAGVILEPIVGNSGFIVP 243 Query: 186 NIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPDILTAGKAIGGGFPVS 245 + F++ L+E T +LL+FDE+ TGF R + + + PD+ T GK IGGG PV Sbjct: 244 DAGFLEGLREITLEHDALLVFDEVMTGF-RIAYGGVQEKFGVTPDLTTLGKIIGGGLPVG 302 Query: 246 VVFLPDHIANKLEEGD---HGSTYGGNPMAMAAVTAACKVIEKENVVEQANQKGQQFSNI 302 I + T GNP+AM A +++ + E +Q ++ S+ Sbjct: 303 AYGGKREIMQLVAPAGPMYQAGTLSGNPLAMTAGIKTLELLRQPGTYEYLDQITKRLSDG 362 Query: 303 LV 304 L+ Sbjct: 363 LL 364 Lambda K H 0.317 0.136 0.385 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: 402 Number of extensions: 14 Number of successful extensions: 5 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: 387 Length of database: 453 Length adjustment: 32 Effective length of query: 355 Effective length of database: 421 Effective search space: 149455 Effective search space used: 149455 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