Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012336169.1 M446_RS31620 aspartate aminotransferase family protein
Query= curated2:Q5JFW3 (362 letters) >NCBI__GCF_000019365.1:WP_012336169.1 Length = 397 Score = 253 bits (645), Expect = 8e-72 Identities = 161/383 (42%), Positives = 213/383 (55%), Gaps = 22/383 (5%) Query: 1 MPLY-RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVA 59 +P Y R ++ RGEG ++ G RYLD AGI VN LGHAHP V ++ Q K+ Sbjct: 6 LPTYARAKVSFERGEGAWLVARDGSRYLDFGAGIAVNALGHAHPHLVEALTEQARKVWHV 65 Query: 60 GPMFEHDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL--ATG----RSEIVAM 113 +FE E E + + L + V+ NSG EA EAAIK AR A G R IV Sbjct: 66 SNLFEIPEGERLAQRLIDATFADVVFFSNSGAEANEAAIKMARKYHAAGGHPERFRIVTF 125 Query: 114 TNAFHGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQG 173 AFHGRTL +++A ++KY EGFGP V GF +P+ +++A AIT ETAA++ EPIQG Sbjct: 126 EGAFHGRTLATIAAGGQQKYIEGFGPKVEGFDQVPYGDLDALAHAITPETAALMIEPIQG 185 Query: 174 EGGIVPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGI 232 EGG+ EF++TLR L + G LLI DEVQ+G+ RTGK A E GV PDI++ KGI Sbjct: 186 EGGLRVVSPEFLRTLRGLCDRHGLLLIMDEVQTGMGRTGKLFAHEWSGVTPDILSAAKGI 245 Query: 233 GNGFPVSLTLTDLEIPR----GKHGSTFGGNPLACRAVATTLRI---------LRRDRLV 279 G GFP+ L E R G HG+TFGGNPLA L + +RR L+ Sbjct: 246 GGGFPMGACLATREAARGMVVGSHGTTFGGNPLAMAVGNAVLDVVLAPGFLEQVRRTGLL 305 Query: 280 EKAGEKFMEFSGERVV-KTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLP 338 K ++ V+ + RG GLM G+ P + A + +LV AG+ V+RLLP Sbjct: 306 LKQRLAALKDRHPGVIAEVRGEGLMTGLRCVVPNTEFAAAARAEHLLVIPAGDNVVRLLP 365 Query: 339 PLIIEGDTLEEARKEIEGVLNDI 361 PLII + EA +E + + Sbjct: 366 PLIIGEAEVAEAVNRLEAASSSL 388 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: 410 Number of extensions: 21 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: 362 Length of database: 397 Length adjustment: 30 Effective length of query: 332 Effective length of database: 367 Effective search space: 121844 Effective search space used: 121844 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 Jul 25 2024. The underlying query database was built on Jul 25 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