Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III
Query= curated2:Q7SI94 (388 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 157 bits (398), Expect = 4e-43 Identities = 107/349 (30%), Positives = 172/349 (49%), Gaps = 36/349 (10%) Query: 16 IKGEGQYVWDEKNNKYLDMHAGHGVAFLGHRNKVIIDHLKKQMEEISTLSLAFDTPIREE 75 + G+G Y+ D +YLD G V+ LGH + +I +++Q+ +++ F T E Sbjct: 17 VAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAE 76 Query: 76 MIKEL-DELKPEDLDNLFLLNSGSEAVELALKIARKI------TKRRKIVAFKNSFHGRS 128 + +L P DL ++ ++ GSEA E A+K+AR+ T RR ++A + S+HG + Sbjct: 77 ALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNT 136 Query: 129 MGALSVTWNKKYREPFEPLIGPVEFLE--YNNVDS---------------------LKSI 165 +GAL+ N R+ F PL+ + + Y VD L+ Sbjct: 137 LGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRLG 196 Query: 166 TEDTAAVIVEPVQGE-GGVIPAKKEFVKSLREVTEKVNALLIIDEVQTGFGRTGKIWAYQ 224 E A + EPV G G +PA + + K +RE+ ++ LLI+DEV G GRTG ++A + Sbjct: 197 PETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFACE 256 Query: 225 HFDIKPDILTAGKAIGGGF-PVSAVFLPNWISEKIEEG----DHGSTYGGNPLAAAAVTA 279 + PDIL K +G G+ P+ A+ I + IE G HG TY G+P+A AA A Sbjct: 257 ADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGLA 316 Query: 280 ACKVAKSEKIAEQAQKKGELFMRILKEKLEDFKIVREIRGLGLMIGIDL 328 + + +++ + GE L + V ++RG GL GI+L Sbjct: 317 VVRALLDRGLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIEL 365 Lambda K H 0.317 0.136 0.386 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: 350 Number of extensions: 25 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: 388 Length of database: 440 Length adjustment: 31 Effective length of query: 357 Effective length of database: 409 Effective search space: 146013 Effective search space used: 146013 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 (21.6 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