Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 239 bits (610), Expect = 1e-67 Identities = 148/381 (38%), Positives = 212/381 (55%), Gaps = 30/381 (7%) Query: 8 LRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDE 67 L L RGEG VWD +GR YLD +AGI LGHAHPE V +S Q+ K+ ++ E Sbjct: 36 LALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVDAISDQIRKLHHVSNLYYIPE 95 Query: 68 REEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFAR------LATGRSEIVAMTNAFHGRT 121 + ++ L+ + V+ NSG EA EAAIK AR L I+ +FHGRT Sbjct: 96 QGQLAAWLTANSCADRVFFCNSGAEANEAAIKLARKHGNTVLEAENPIILTAQASFHGRT 155 Query: 122 LGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAK------EAITKETAAVIFEPIQGEG 175 L +++AT + KY +GF PLV GF+++P+N++ A + +A + AA++ EP+QGEG Sbjct: 156 LAAVTATGQPKYHKGFQPLVQGFRYVPYNDLAALEATLAELDAAGETVAAILLEPLQGEG 215 Query: 176 GIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGN 234 G+ P D + + +R L + LLI DEVQ G+ R+G+ E+ G+ PD T+ KG+G Sbjct: 216 GVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLWGYENLGIEPDAFTVAKGLGG 275 Query: 235 GFPVSLTLTDLE---IPRGKHGSTFGGNPLACRAVATTLRILRRDRL---VEKAGEKFME 288 G P+ L + G+H STFGGNPLACRA +++ RD+L V+ GE+ Sbjct: 276 GVPIGALLVKASCNILQAGEHASTFGGNPLACRAGLAIAQVMERDQLLANVQARGEQLRA 335 Query: 289 FSGERVVK-------TRGRGLMIGIVLRRPAG----NYVKALQERGILVNTAGNRVIRLL 337 E V + RG GL+ G+VLR VKA E+G+L+ AG V+R + Sbjct: 336 GLQELVDRYPNLLAGVRGWGLINGLVLRNDPNVTPIALVKAAIEQGLLLVPAGAEVVRFV 395 Query: 338 PPLIIEGDTLEEARKEIEGVL 358 PPLI+ ++EA E L Sbjct: 396 PPLIVSAAEIDEALAMTERAL 416 Lambda K H 0.320 0.140 0.410 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: 359 Number of extensions: 22 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: 362 Length of database: 422 Length adjustment: 31 Effective length of query: 331 Effective length of database: 391 Effective search space: 129421 Effective search space used: 129421 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