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 N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase
Query= metacyc::MONOMER-18314 (387 letters) >FitnessBrowser__Dyella79:N515DRAFT_3308 Length = 411 Score = 236 bits (601), Expect = 1e-66 Identities = 139/397 (35%), Positives = 215/397 (54%), Gaps = 22/397 (5%) Query: 4 IQLYGDRGLTIVKGEAQYVWDIEGRRYLDFHTGIGVAFLGHRNPIILEYLKNQLENISIL 63 + +Y R + + G+ VWD EGR Y+D GI V LGH++P +++ L Q + Sbjct: 19 LPVYRPREVVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHS 78 Query: 64 STSFSTP----IKDEMLQALDKVKPDKMDNAMLLNSGTEAVEAALKTARKITGRKK---- 115 S F T + +E++QA + L NSGTEA EAA+K RK K Sbjct: 79 SNVFYTEPPLHLAEELVQASGFA-----ERVFLCNSGTEANEAAIKLVRKWAASKGRAPE 133 Query: 116 ---IIAFKNAFHGRTAGSLSVTWNKKYREPFEPLVGPVEFLTFNNIEDLSKI--DNETAA 170 I+ F+ +FHGRT +++ T KY+E +EPL G +L FN++ L + AA Sbjct: 134 QRVILTFRGSFHGRTLAAVTATAQPKYQENYEPLPGGFRYLDFNDVAGLEAAFAQGDVAA 193 Query: 171 VIVEPIQGESGVIPANIEFMKALKEKTENTGSLLIFDEIQTGFGRTGKLWAYKHYNIVPD 230 V++EP+QGE GV+PA+ F++ +E + +LL+ DEIQ G GRTG L+A+ + PD Sbjct: 194 VMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQDGVTPD 253 Query: 231 ILTAGKAIGGGFPVSVVFLPDHIANKLEEGDHGSTYGGNPMAMAAVTAACKVIEKENVVE 290 I+T KA+G GFP+ + +A ++ G HG+T+GGNPMA A A + + ++ Sbjct: 254 IVTLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLASAELMA 313 Query: 291 QANQKGQQFSNILVKNLADLKVVREVRGKGLMIGIDI----RFQPGQVLKYLQEKGILAV 346 ++ Q + L +LK+ EVRG+GLM+G + + + G+VL + G+L + Sbjct: 314 NVAKQAQALRDGLAAIDGELKLFAEVRGRGLMLGAVLAEAYKGRAGEVLDHAAAHGLLVL 373 Query: 347 KAGSTVIRFLPSYLITYENMEEASNVLREGLLKIENK 383 +AG V+RF+P IT ++ E LR L K Sbjct: 374 QAGPDVLRFVPPLNITDADLAEGLARLRAALADFVGK 410 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: 354 Number of extensions: 11 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: 411 Length adjustment: 31 Effective length of query: 356 Effective length of database: 380 Effective search space: 135280 Effective search space used: 135280 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