Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= curated2:Q9YBY6 (388 letters) >FitnessBrowser__Dyella79:N515DRAFT_1751 Length = 467 Score = 151 bits (382), Expect = 3e-41 Identities = 136/420 (32%), Positives = 192/420 (45%), Gaps = 55/420 (13%) Query: 16 LRIVKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQAREL--VAASSSFST 73 L IV+G ++ D GR+YLD + GH+NP I A+ +Q L V + Sbjct: 48 LPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTHE 107 Query: 74 PSLEEALTEFSRIAPPWAEEIVFLNTGTEAVEAALKAA---WLATG---KRGIVALKNSF 127 P++E A ++I P E + + G+ A+E ALK + WL G K +AL S+ Sbjct: 108 PAIELA-ERLAQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGSY 166 Query: 128 HGRTLASLSVTWNPRYRRG-VPVLDTRFLSPSTDP-----------------GEVEKLVP 169 HG TL +LSV+ YR+ P+L T L+PS D GE+ L+ Sbjct: 167 HGETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLLE 226 Query: 170 E---DTAAIIVEP-IQGEGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWA 225 + +T A+IVEP +Q GG+ + LR D G I DEI GFGRTG ++A Sbjct: 227 QHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLFA 286 Query: 226 HESLGVEPDIMTAGKSIAGG-LPASAVLSR----EGVLATLASGR---HGSTHAANPLSM 277 E GV PD M K + GG LP SAVL+ E A +G+ H ++ NPL+ Sbjct: 287 CEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLAC 346 Query: 278 AAVAAASRFLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVELRLDPGP 337 A A R+E V ++ R A L L E + V VR G++ VEL D Sbjct: 347 RAALATLDIFRDEPVLERNRELAAHLARRLAPLREHPQ-VADVRQTGMIAAVELVRDKAT 405 Query: 338 VLRCLQESERVL-----------ALRSGATVVRLLPPYSISRED----AEMVVYGLERCI 382 E R L LR VV +PPY +S ++ ++ + G+ER I Sbjct: 406 RAPYPSEERRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLVDVAIAGIERAI 465 Lambda K H 0.319 0.136 0.398 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: 387 Number of extensions: 14 Number of successful extensions: 4 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: 467 Length adjustment: 32 Effective length of query: 356 Effective length of database: 435 Effective search space: 154860 Effective search space used: 154860 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: 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