Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 (uncharacterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= curated2:Q9RW75 (429 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 162 bits (410), Expect = 2e-44 Identities = 133/424 (31%), Positives = 202/424 (47%), Gaps = 54/424 (12%) Query: 31 VRGQGATVWDENGRSYIDCVVGYGVATLGHSHPDVVKAVQEQAGKLMVMPQTVPNDKRAE 90 V G G + D NG+ Y+D G V+ LGHS +V+ AVQEQ GKL + AE Sbjct: 17 VAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAE 76 Query: 91 FLQEL-VGVLPQGLDRVFLCNSGTEAMEAAKKFAITA------TGRSRFVSMKRGFSGRS 143 L +L + P L RV+ + G+EA EAA K A T R ++ ++ + G + Sbjct: 77 ALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNT 136 Query: 144 LGALSFTWEPKYREPFGDAVDNKS-----VDFVTYGN-----------LDELRAAVT--- 184 LGAL+ R+ F + + S ++V G+ +EL A + Sbjct: 137 LGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRLG 196 Query: 185 -EQTAAVIMEPVQGE-GGVRPASAEFIQEARRITREKGALLILDEIQTGFCRTGKMFACE 242 E A + EPV G G PA + + R I + G LLILDE+ G RTG +FACE Sbjct: 197 PETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFACE 256 Query: 243 HFGVIPDGMTLAKAI-AGGTPTAAFAMMSEVADRMPAGG----HGTTFGGNPLSMAAGVA 297 GV PD + +AK + AG P A ++ D + G HG T+ G+P++ AAG+A Sbjct: 257 ADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGLA 316 Query: 298 SLRAMKREGLAEQAREKGAYMMDKL--RAIQSPKIREVRGLGLMIGVEL---KEKSAPY- 351 +RA+ GL +++ E G + L R Q P + ++RG GL G+EL +E P+ Sbjct: 317 VVRALLDRGLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRESKTPFD 376 Query: 352 --------IHAMEHDEGVLC--LAAT-----PLVVRFLPPAVISKEQIDQVVAAFERVLN 396 + + G++C +A T + PP ++S++QI ++ E L+ Sbjct: 377 PGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHILLAPPFILSEDQIGEITDKLEVALD 436 Query: 397 NVNP 400 V P Sbjct: 437 QVLP 440 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: 460 Number of extensions: 18 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: 429 Length of database: 440 Length adjustment: 32 Effective length of query: 397 Effective length of database: 408 Effective search space: 161976 Effective search space used: 161976 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