Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate GFF900 PGA1_c09150 adenosylmethionine-8-amino-7-oxononanoate aminotransferase BioA
Query= curated2:Q8ZV07 (383 letters) >FitnessBrowser__Phaeo:GFF900 Length = 432 Score = 104 bits (260), Expect = 4e-27 Identities = 105/393 (26%), Positives = 174/393 (44%), Gaps = 43/393 (10%) Query: 26 DKGQRYIDCNTNHGVVFLGHANPKIVEAVKKQVEEIWAVPLNFATPARERFIEEFSKLL- 84 D G R ID ++ + GH NP I A+ Q++ + V T + I+ KLL Sbjct: 43 DDGTRLIDAMSSWWCMMHGHRNPAITSAIHAQLDTLPHVMFGGLT--HDPAIDLGRKLLE 100 Query: 85 --PPKFGVVFLQNTGTEAVEVAIKIAKKVTR------KPTIVAFTNSFHGRTMGSLSIT- 135 P +F ++G+ +VEVA+K+A + + + +HG T ++S+ Sbjct: 101 ITPESLTRIFYCDSGSVSVEVAMKMAVQYQHAIGQPERKEFATIRSGYHGDTWKAMSVCD 160 Query: 136 ----WNEKYKKAFEPLY----PHVRFGKFNVPHEVDKLIGE----------DTCCVVVEP 177 + ++ A + P VR + +GE ++EP Sbjct: 161 PDTGMHHLFQGALSVQHFVSRPPVRIHEDWSDDPAQNGLGELRAVLEAGQDKIAAFILEP 220 Query: 178 I-QGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWAFQKYGVEPDIFTA 236 + QG GG+ PE+L R G LLIFDE+ TGFGRTGA++A EPDI Sbjct: 221 VVQGTGGMYFYHPEYLNQARALCDELGILLIFDEIATGFGRTGALFATNFCDAEPDIICL 280 Query: 237 GKPVAGG-LPIGLAVAREDFGDVFEPGE-----HGSTFAGNAVVMAAAAAASRLLREED- 289 GK + GG + + + + G HG T+ N + AAA A+ LL +D Sbjct: 281 GKGLTGGHISFACTMTNDRVAEGVGGGNPGIFMHGPTYMANPLACAAAKASLDLLTGQDW 340 Query: 290 ---VPGRAERIGAELAKALGDTGSRLAVRVKGMGLMLGLELRVKADQFIQPLLERGVMAL 346 V G AE++ +ELA A + + VRV G ++ ++ V AD+ + GV Sbjct: 341 RGTVSGIAEQMQSELATA-RELPNVADVRVLGAIGVIEMKHAVSADEAHARAHDMGVFLR 399 Query: 347 TAGVNTLRFLPPYMISKEDVEVVHAAVTEVLKK 379 G N + +PP++ + + + + A + + ++ Sbjct: 400 PFGKN-IYTMPPFITTPDQLSQITAGMLRLARE 431 Lambda K H 0.320 0.138 0.408 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: 396 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 383 Length of database: 432 Length adjustment: 31 Effective length of query: 352 Effective length of database: 401 Effective search space: 141152 Effective search space used: 141152 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