Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012506718.1 PAES_RS10875 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:Q9YBY6 (388 letters) >NCBI__GCF_000020625.1:WP_012506718.1 Length = 428 Score = 124 bits (312), Expect = 4e-33 Identities = 124/388 (31%), Positives = 190/388 (48%), Gaps = 55/388 (14%) Query: 29 DSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQAREL--VAASSSFSTPSLEEALTEFSRI 86 + GRK +D + AA G+++P + AV RQ + V P+++ A + + Sbjct: 41 EDGRKLVDGMSSWWAAVHGYNHPVLNHAVTRQLDSMSHVMFGGLTHEPAVKLA-GQLIEL 99 Query: 87 APPWAEEIVFLNTGTEAVEAALKAA---WLATG---KRGIVALKNSFHGRTLASLSVTWN 140 P +++ F ++G+ +VE A+K A W A G KR ++ +++ +HG T ++SV + Sbjct: 100 TPEPLQKVFFSDSGSVSVEVAIKMALQYWQAAGLSRKRRLLTVRSGYHGDTFGAMSVC-D 158 Query: 141 PRYRRGVPVLDTRFLSPST-------------DPGEVEKLVP------EDTAAIIVEPI- 180 P G+ L T L+ + +E L E AA+I+EP+ Sbjct: 159 PD--TGMHSLFTGMLAEQLFAEAPQCGFDAAWNENGIEDLHQKLRQHHEAVAAVIIEPVV 216 Query: 181 QGEGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHESLGVEPDIMTAGK 240 QG GG+ LRE D G LLIFDEI TGFGRTG+++A E GV PDIM GK Sbjct: 217 QGAGGMRFYSPHYLIRLRELCDEYGVLLIFDEIATGFGRTGKMFALEHAGVVPDIMCVGK 276 Query: 241 SIAGG-LPASAVLSREGVLATLASGR-----HGSTHAANPLSMAAVAAASRFL----REE 290 ++ GG + +A L+ + V T++S HG T ANPL+ + +A+ L E+ Sbjct: 277 ALTGGYMTLAATLAADHVADTISSAEPGLFMHGPTFMANPLACSVASASIDLLCSRDWEQ 336 Query: 291 GVPDKARAAGALLEGLLR-DRIEGLRLVRGVRGEGLMLGVEL--RLDPGPVLRCLQESER 347 V D GAL +GL R G+ VR + G+ VEL +D V ER Sbjct: 337 EVQD---IQGALQDGLSPCSRFSGVHDVRVLGAIGV---VELCQPVDMAAVQNFF--VER 388 Query: 348 VLALRSGATVVRLLPPYSISREDAEMVV 375 +R ++ L+PP+ IS +EMV+ Sbjct: 389 GAWVRPFGRLIYLMPPFIIS--PSEMVI 414 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: 359 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 388 Length of database: 428 Length adjustment: 31 Effective length of query: 357 Effective length of database: 397 Effective search space: 141729 Effective search space used: 141729 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 10 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