Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate WP_025272511.1 HALAL_RS0102620 aspartate aminotransferase family protein
Query= curated2:Q9RW75 (429 letters) >NCBI__GCF_000527155.1:WP_025272511.1 Length = 417 Score = 236 bits (603), Expect = 8e-67 Identities = 152/402 (37%), Positives = 213/402 (52%), Gaps = 31/402 (7%) Query: 28 VVMVRGQGATVWDENGRSYIDCVVGYGVATLGHSHPDVVKAVQEQAGKLMV-MPQTVPND 86 VV G+G ++D +GR Y+D G GV + GH HP VV+A QEQ GKL+ TV + Sbjct: 14 VVADHGEGVYLYDADGRRYLDFTAGIGVTSTGHCHPHVVQAAQEQVGKLIHGQYTTVMHQ 73 Query: 87 KRAEFLQELVGVLPQGLDRVFLCNSGTEAMEAAKKFAITATGRSRFVSMKRGFSGRSLGA 146 E + L VLP GLD +F NSG+EA+EAA + + ATGR V + GF GR++ Sbjct: 74 PLLELTRRLGDVLPAGLDSLFFSNSGSEAVEAALRLSRQATGRPNIVVFQGGFHGRTVAT 133 Query: 147 LSFTWEPK-------------YREPFGDAV----DNKSVDFVTYGNLDELRAAVTE--QT 187 + T + PF A D + LD L A VT +T Sbjct: 134 ATLTTSGTRFSAGISPLMSGVHMAPFPYAYRYGWDESTATEFALRELDYLFATVTSPAET 193 Query: 188 AAVIMEPVQGEGGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTGKMFACEHFGVI 247 AA +EPV GEGG PA+ EF+ R+ E G LL+LDEIQTGF RTGK + +HFGV Sbjct: 194 AAFFIEPVLGEGGYVPANPEFLAGLRQRADEHGILLVLDEIQTGFGRTGKFWGHDHFGVH 253 Query: 248 PDGMTLAKAIAGGTPTAAFAMMSEVADRMPAGGHGTTFGGNPLSMAAGVASLRAMKREGL 307 PD + +AK +A G P + A E+ + G G T+GGN ++ AA VA+L ++REGL Sbjct: 254 PDVVLIAKGLASGFPLSGMATSEELMSQAWPGSQGGTYGGNAVACAAAVATLDVIQREGL 313 Query: 308 AEQAREKGAYMMDKLRAI--QSPKIREVRGLGLMIGVEL---------KEKSAPYIHAME 356 + A ++G +++ R I ++P I +VRGLGLM+G E A A Sbjct: 314 VDNAADRGRQLLEGARHIGEKTPLIGDVRGLGLMVGSEFTTPDGQPDTATAQAAQKEAAA 373 Query: 357 HDEGVLCLAATPLVVRFLPPAVISKEQIDQVVAAFERVLNNV 398 +L A VVR +PP V+ Q+D+ + + V+++V Sbjct: 374 RGLMLLTCGAHMNVVRMIPPLVVDAAQVDEALDIWSEVVSSV 415 Lambda K H 0.317 0.132 0.380 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: 448 Number of extensions: 23 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: 429 Length of database: 417 Length adjustment: 32 Effective length of query: 397 Effective length of database: 385 Effective search space: 152845 Effective search space used: 152845 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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