Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate AO353_15640 AO353_15640 acetylornithine aminotransferase
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15640 Length = 391 Score = 212 bits (540), Expect = 1e-59 Identities = 126/382 (32%), Positives = 198/382 (51%), Gaps = 13/382 (3%) Query: 8 YREYGIRIVKGFMQYVWDDKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVPLN 67 Y+ + +G +WD G+ Y+D V +GH++PK+V A+ +Q + Sbjct: 10 YQPLALSFTRGLGTRLWDQAGREYLDAVAGVAVTNVGHSHPKVVSAISEQAGLLLHTSNL 69 Query: 68 FATPARERFIEEFSKLLPPKFGVVFLQNTGTEAVEVAIKIAK-----KVTRKPTIVAFTN 122 ++ ++R + ++L VF N+G EA E A+K+A+ K +P +V N Sbjct: 70 YSIDWQQRLAHKLTQL--SGLDRVFFNNSGAEANETALKLARLYGWHKGVEQPLVVVMEN 127 Query: 123 SFHGRTMGSLSITWNEKYKKAFEPL---YPHVRFGKFNVPHEVDKLIGEDTCCVVVEPIQ 179 +FHGRT+G+LS + + F+ L + V FG + + G+ V++EPIQ Sbjct: 128 AFHGRTLGTLSASDGPAVRLGFQELPGDFIKVPFGDLAALDKAHQTHGQRIVAVLMEPIQ 187 Query: 180 GEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTAGKP 239 GE GV A P +LKALRE R+ LL+ DE+QTG GRTG +AFQ G+ PD+ T K Sbjct: 188 GESGVQLALPGYLKALRELCNRRNWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKG 247 Query: 240 VAGGLPIGLAVAREDFGDVFEPGEHGSTFAGNAVVMAAAAAASRLLREEDVPGRAERIGA 299 + G+PIG +AR ++F PG HGSTF GN + ++ E+ + A+R G Sbjct: 248 LGNGVPIGACLARGKAAELFTPGSHGSTFGGNPLACRVGCTVLEIIEEQGLLENAKRQGE 307 Query: 300 ELAKALGD--TGSRLAVRVKGMGLMLGLEL-RVKADQFIQPLLERGVMALTAGVNTLRFL 356 L L GS + ++G GLM+G+EL R D + + G++ T+R L Sbjct: 308 RLLARLHAELDGSPQVLAIRGQGLMIGIELARPIRDLTLIAARDHGLLINVTRGKTIRLL 367 Query: 357 PPYMISKEDVEVVHAAVTEVLK 378 PP I + +VE++ V V++ Sbjct: 368 PPLTIDEREVEMIVRGVGRVVR 389 Lambda K H 0.320 0.138 0.408 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: 370 Number of extensions: 23 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: 383 Length of database: 391 Length adjustment: 30 Effective length of query: 353 Effective length of database: 361 Effective search space: 127433 Effective search space used: 127433 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