Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__azobra:AZOBR_RS19025 Length = 389 Score = 241 bits (614), Expect = 3e-68 Identities = 150/377 (39%), Positives = 206/377 (54%), Gaps = 32/377 (8%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 MP Y R + RGEG Y++ GRR+LD AG+ VNVLGHA+P V ++ Q K+ Sbjct: 6 MPTYARADIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHT 65 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARLA------TGRSEIVAM 113 +F +E + + L+ + V+ NSG EA E K R R+ I+ Sbjct: 66 SNLFRVAGQESLAKRLTEATFADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITF 125 Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173 AFHGRTL ++SA ++K +GFGPL+ GF +PF ++EA + A+T ETA + EPIQG Sbjct: 126 EQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFGDLEAVRNAVTDETAGICLEPIQG 185 Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232 EGGI EF++ LR++ ++ G LL DE+Q G+ RTGK A E G+ PD++ + KGI Sbjct: 186 EGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEWAGITPDVMAVAKGI 245 Query: 233 GNGFPVSLTLTDLE----IPRGKHGSTFGGNPLACRAVATTL-------------RI--L 273 G GFP+ L + + G HGST+GGNPLA L RI L Sbjct: 246 GGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVLEPGFLDHVQRIGGL 305 Query: 274 RRDRLVEKAGEKFMEFSGERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRV 333 +DRL E F G RG+GLM+G+ G+ V AL+ G+L AG+ V Sbjct: 306 LQDRLAGLVAENPAVFKG-----VRGKGLMLGLACGPAVGDVVVALRANGLLSVPAGDNV 360 Query: 334 IRLLPPLIIEGDTLEEA 350 +RLLPPL I +EEA Sbjct: 361 VRLLPPLNIGEAEVEEA 377 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: 401 Number of extensions: 26 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: 362 Length of database: 389 Length adjustment: 30 Effective length of query: 332 Effective length of database: 359 Effective search space: 119188 Effective search space used: 119188 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