Align Putative [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:Q5JFW3 (362 letters) >FitnessBrowser__Phaeo:GFF2829 Length = 440 Score = 149 bits (377), Expect = 1e-40 Identities = 135/423 (31%), Positives = 189/423 (44%), Gaps = 71/423 (16%) Query: 11 VRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE 70 V G+G Y+ D G+RYLD G V+ LGH+ E + + Q+ K+ A F E E Sbjct: 17 VAGDGCYLIDANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAE 76 Query: 71 MLEEL---SHWVDYEYVYMGNSGTEAVEAAIKFARL------ATGRSEIVAMTNAFHGRT 121 L +L D VY + G+EA EAAIK AR T R ++A ++HG T Sbjct: 77 ALADLLISQAPGDLHRVYFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNT 136 Query: 122 LGSLSATWKKKYREGFGPLVPGFKHIP---------------------FNNVEAAKEAIT 160 LG+L+A R+ F PL+ HI N +EA + Sbjct: 137 LGALAAGGNAWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRLG 196 Query: 161 KETA-AVIFEPIQG-EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIE 217 ET A + EP+ G G VPA E + K +R++ + G LLI DEV G+ RTG A E Sbjct: 197 PETVMAFMAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFACE 256 Query: 218 HYGVRPDIVTMGKGIGNGF-PVSLTLTDLEIPRG--------KHGSTFGGNPLACRAVAT 268 GV PDI+ + KG+G G+ P+ L +I +HG T+ G+P+A A Sbjct: 257 ADGVAPDILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGLA 316 Query: 269 TLRILRRDRLVEKAGEKFMEFSGERVVK---------TRGRGLMIGIVL------RRP-- 311 +R L LV+++ E V + RGRGL GI L + P Sbjct: 317 VVRALLDRGLVQRSAEMGETLHAALVARFGQHPHVGDLRGRGLFRGIELVADRESKTPFD 376 Query: 312 -----AGNYVKALQERGIL-VNTAGNR------VIRLLPPLIIEGDTLEEARKEIEGVLN 359 AG KA E G++ AG R I L PP I+ D + E ++E L+ Sbjct: 377 PGLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHILLAPPFILSEDQIGEITDKLEVALD 436 Query: 360 DIL 362 +L Sbjct: 437 QVL 439 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: 401 Number of extensions: 22 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: 440 Length adjustment: 31 Effective length of query: 331 Effective length of database: 409 Effective search space: 135379 Effective search space used: 135379 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 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