Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.-; EC 2.6.1.118 (characterized, see rationale)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
Query= uniprot:Q5JFW3 (362 letters) >FitnessBrowser__Marino:GFF3099 Length = 404 Score = 246 bits (627), Expect = 1e-69 Identities = 154/376 (40%), Positives = 216/376 (57%), Gaps = 25/376 (6%) Query: 11 VRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE 70 VRGEG +WD++GR ++DL GI V LGH+HP V + Q EKI + ++ Sbjct: 27 VRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEPALR 86 Query: 71 MLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL------ATGRSEIVAMTNAFHGRTLGS 124 + + L E V+ NSG EA EAA K AR ++EI++ N+FHGRTL + Sbjct: 87 LAKTLCDLTFAERVFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHGRTLFT 146 Query: 125 LSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKE-TAAVIFEPIQGEGGIVPADEE 183 +S + KY EGF P G H FN++E+ K+ I+KE T A++ EPIQGEGG++P D+ Sbjct: 147 VSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAIVVEPIQGEGGVMPGDQA 206 Query: 184 FVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGFPVSLTL 242 F++ LRDL ++ ALL+ DEVQSG+ R+G F A + YGV PDI++ KG+G GFPV+ L Sbjct: 207 FLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQMYGVVPDILSSAKGLGGGFPVAAML 266 Query: 243 TDLEIPR----GKHGSTFGGNPLAC----RAVATTLR--ILRRDRLVEKAGEKFMEFSGE 292 T ++ G HGST+GGN LAC R V T + IL+ + K M GE Sbjct: 267 TTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILKGVKARSDKLRKGMMDIGE 326 Query: 293 R---VVKTRGRGLMIGIVL----RRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGD 345 R + RG GL++G VL + A +++ A E G++V AG VIRL P LII Sbjct: 327 RYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAPSLIIPEP 386 Query: 346 TLEEARKEIEGVLNDI 361 +E A + E + + Sbjct: 387 DIELALERFEAAVKKL 402 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: 391 Number of extensions: 24 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: 404 Length adjustment: 30 Effective length of query: 332 Effective length of database: 374 Effective search space: 124168 Effective search space used: 124168 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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