Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate SMa2400 SMa2400 diaminobutyrate--2-oxoglutarate aminotransferase
Query= curated2:Q9RW75 (429 letters) >FitnessBrowser__Smeli:SMa2400 Length = 470 Score = 217 bits (553), Expect = 5e-61 Identities = 156/419 (37%), Positives = 218/419 (52%), Gaps = 56/419 (13%) Query: 28 VVMVRGQGATVWDENGRSYIDCVVGYGVATLGHSHPDVVKAVQEQAGK---LMVMPQTVP 84 V + G V D +GRSY+DC+ G G LGH+HP+V++ +Q+ G L + T P Sbjct: 51 VALKSASGCIVTDVDGRSYLDCLAGAGTLALGHNHPEVIETLQQVLGSGLPLHTLDLTTP 110 Query: 85 NDKRAEFLQELVGVLPQGLD---RVFLCN-SGTEAMEAAKKFAITATGRSRFVSMKRGFS 140 R F+ ++ G LP GL ++ C+ SGT+A+EAA K A TATGR+ VS + + Sbjct: 111 VKDR--FVSDIFGTLPAGLRDEAKIQFCSPSGTDAVEAAIKLAKTATGRTDLVSFRGAYH 168 Query: 141 GRSLGALS--------------------FTWEPKYREPFGDAVDNKSVDFVTYGN--LDE 178 G S G+LS F + YR PFG + + Y L + Sbjct: 169 GMSQGSLSLMGSLGPKASVGQLVPGAHFFPYPYAYRCPFGRGGNETATLAAEYFERALRD 228 Query: 179 LRAAVTEQTAAVIMEPVQGEGGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTGKM 238 + + AAVI+E VQGEGGV PA E+++ RR+TR+ G LI+DE+Q+G RTG Sbjct: 229 PEGGIN-RPAAVILEAVQGEGGVIPAPVEWLRAVRRVTRDLGIPLIVDEVQSGVGRTGSF 287 Query: 239 FACEHFGVIPDGMTLAKAIAGGTPTAAFAMMSEVADRMPAGGHGTTFGGNPLSMAAGVAS 298 +A + G+IPD + L+KAI GG P A + E D G H TF GN L+MAAG + Sbjct: 288 YAFQKAGIIPDVVVLSKAIGGGLPLAV-VIYREDLDLWKPGAHAGTFRGNQLAMAAGSKT 346 Query: 299 LRAMKREGLAEQAREKGAYMMDKLR--AIQSPKIREVRGLGLMIGVELKEKSA------- 349 L ++RE L E+A G + L A Q+P I EVRG GLM+GVE+ + Sbjct: 347 LEIIERERLVERAAIAGRRLRANLERIAAQTPYIGEVRGEGLMLGVEVVDPEGLPDALGH 406 Query: 350 -----PYIHAMEHD---EGVLCLAATPL--VVRFLPPAVISKEQIDQV----VAAFERV 394 ++H+ G++ V+R LPP VIS +IDQV AAFER+ Sbjct: 407 PPHGQEIARMIQHEMFRAGIILETGGRFGSVLRLLPPLVISDAEIDQVSGALAAAFERL 465 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: 486 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 429 Length of database: 470 Length adjustment: 33 Effective length of query: 396 Effective length of database: 437 Effective search space: 173052 Effective search space used: 173052 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: 51 (24.3 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